Mario & Luigi: Superstar Saga + Bowser's Minions

Mario & Luigi: Superstar Saga + Bowser's Minions is a game in the Mario & Luigi series released for the Nintendo 3DS worldwide in October 2017 and in South Korea on April 12, 2018. It is an enhanced remake of the 2003 Game Boy Advance game Mario & Luigi: Superstar Saga. The game has an added story called Minion Quest: The Search for Bowser, which takes place simultaneously with the main story. The game has amiibo support for the Minion Quest mode, where the Koopa Troopa, Goomba, and Boo amiibo are compatible. The game is the first remake in the Mario & Luigi series, the third game in the series to be released for the Nintendo 3DS, and the sixth game in the series overall. Unlike the previous two games, the environments are no longer rendered in 3D. As a result of this, the game is only playable in 2D.

Mario & Luigi: Superstar Saga
The remake of Mario & Luigi: Superstar Saga has updated graphics, soundtrack, and controls, looking visually similar to Mario & Luigi: Dream Team and Mario & Luigi: Paper Jam. The story is mainly the same as it was in the original game. However, some additions and alterations to the gameplay have also been made.

Gameplay

 * The Mario Bros. game is no longer included, being replaced with a new side-mode, Minion Quest: The Search for Bowser, which is accessible via the suitcase after Mario and Luigi spot Captain Goomba, who is seen running off after Fawful, just before reaching Beanbean Castle Town.
 * Pressing in the overworld makes both Bros. jump or swim simultaneously.
 * The line of the Koopa Troopa in the Koopa Cruiser originally telling the player about switching places was changed to inform about this mechanic.
 * Mario and Luigi's positions can no longer be switched manually. Instead, they switch automatically when selecting a move.
 * In the original game, using the Hammer or Hand Powers on the other brother before unlocking the skill linked to it results in an animation where the brother in front gets angry and scolds the other. In the remake, nothing happens when doing so.
 * Cutscenes can be sped up with, or with the icon on the touch screen.
 * The game now has many new features due to the added second screen.
 * Mario & Luigi's passports showing their level and stats are displayed in battle. When afflicted with a status ailment, a page slips out from that brother's passport to display its name.
 * A tutorial for attacks is displayed in battle similar to the one in Mario & Luigi: Paper Jam.
 * In the overworld, the touch screen can be used to switch between moves like the High Jump or the Spin Jump.
 * The player can also press a button on the touchscreen to display a zoomable mini-map where they can also place pins. The player is given twenty pins for each area and can remove a pin by tapping on it twice.
 * Mario and Luigi are now able to swim high while underwater.
 * Heart Blocks are present in every version of the game unlike in the original, where only the Japanese version featured them, and are far more numerous.
 * Similarly to Mario & Luigi: Dream Team and Mario & Luigi: Paper Jam, saving can now be done at any point on the overworld.
 * The post-battle screen is now similar to the ones used since Mario & Luigi: Bowser's Inside Story and this time, the player should press to collect the EXP and coins.
 * There is now a shades-wearing Hoohooligan merchant behind Blablanadon's nest in Hoohoo Village. He initially sells a set of two Nuts for 72 coins, and when the player returns before heading to Bowser's Castle, he offers sell an Ultra Mushroom, an Ultra Syrup, an Ultra Nut and a 1-Up Super for 750 coins.
 * There is now a Beanish character in Beanbean Castle Town that allows the player to scan compatible amiibo to obtain stamps.
 * The shopkeeper of the information booth no longer sells information to the brothers, and instead looks at the player's records, awarding items based on their progress with blocks, beans, the number of battles won, the number of enemies defeated, the number of Excellent attacks done and the number of battles fled from.
 * The game can now be saved after defeating the final boss.

Menu

 * The menu screen features a guide option, showing how certain actions are performed similar to Mario & Luigi: Paper Jam.
 * This function is also available in battle via the bottom screen.
 * The percentage and amounts of beans and ? Blocks found can also be viewed in the menu screen's Records section along with a summary of the current story, called "The Story So Far".
 * A music option was added in the Records section. Unlike in the previous entries, it is not accessible from the title screen but from the in-game menu screen. The player can also listen to the music from the original version of Mario & Luigi: Superstar Saga in addition to the one from this game, the latter's tracks having "DX" at the end of the name.
 * Options have also been moved from the title screen to the menu screen.
 * Easy Mode from Mario & Luigi: Paper Jam is added, and can be found on the menu screen.
 * There are now only two save files instead of three.

Items

 * Boo Biscuits are included in this game, behaving as they did from Mario & Luigi: Dream Team and Mario & Luigi: Paper Jam.
 * Many bosses now drop new gear such as Hoohooros dropping the Hoohooros Slacks or Rookie dropping the Rookie Badge.
 * Most bosses now always drop their items or gear when defeated.
 * Enemies can now drop a third item that can only be obtained from the Game Boy Horror SP.
 * Accessories can now be obtained throughout the entire game and not just from Professor E. Gadd.
 * Some items heal a different amount of HP or BP than they did in the original game:
 * Mushrooms heal 30 HP instead of 25.
 * Ultra Mushrooms heal 80 HP instead of 120.
 * Ultra Nuts heal 65 HP instead of 100.
 * Syrups heal 15 BP instead of 20.
 * Super Syrups heal 35 BP instead of 40.
 * Ultra Syrups heal 60 BP instead of 100.
 * Each blend in Starbeans Cafe requires less beans, from 25 (25 for single bean, 15/10 for two beans) to 10 (10 for single bean, 6/4 for two beans), and the stat boosts given are reduced by half.
 * Because of this, the player can obtain all seven of E. Gadd's accessories much sooner.
 * The Great Force now resembles the Triforce and gives the traditional item jingle from The Legend of Zelda series.
 * The rare item drop affect from the Game Boy Horror SP now only applies to the bro who has it equipped, rather than affecting both regardless of who has it equipped. The bro who does not have it equipped now can only force a rare drop through a Bros. attack, or countering a counterattack caused by a Bros. attack.

Badges

 * The Mush Badge A and Mush Badge AA deal less damage than in the original game.

Battles

 * Battle statistics for Mario, Luigi, and enemies have changed, generally increasing the difficulty.
 * Mario and Luigi now jump twice on an enemy if a solo jump's action command is entered correctly, just like in the previous installments since Mario & Luigi: Bowser's Inside Story.
 * Bros. Attacks no longer have the three Modes, but have "Normal" and "Easy" difficulties, the latter version being more lenient with button inputs for a Bros. Attack while requiring more Bros. Points.
 * Bros. Attacks have been tweaked, some having different attack properties, while some have new button inputs.
 * Advanced Bros. Attacks are now separately selected from the original Bros. Attacks, have "Super" to their name (Super Splash Bros., Super Bounce Bros.), and cost more Bros. Points to use.
 * All battle backgrounds now scroll whenever Mario or Luigi use a Bros. Attack.
 * The Emergency Guard from Mario & Luigi: Paper Jam is added.
 * The Solo-Attack-Command Block is replaced with separate Command Blocks for Jump, Hammer, and Hand-Attacks.
 * When Mario or Luigi strike an enemy with their hammers before initiating battle, it no longer makes them dizzy; instead, they take damage and their speed is dropped.
 * Hand Powers can also be used to perform first strikes. Aside from taking damage, Firebrand can burn enemies and Thunderhand can make them dizzy.
 * Bosses now turn red (or different colors) when low on health, as in Paper Jam. Some bosses now have altered attack patterns or new attacks:
 * When low on health, Trunkle covers the tree on its head with both hands, making it impervious to attacks.
 * Some enemies can now take critical damage from Jump and Hammer attacks in addition to Fire and Thunder attacks.
 * Clumphs now take critical damage from Mario's Firebrand attacks, especially the Fire Bros. attack.
 * The number of turns it takes for Time Bob-ombs to explode in Roy's battle is increased from eight to nine, while in Wendy's and Larry's, it is reduced to seven and five, respectively.
 * Luigi thinks of all the "Super" versions of his Bros. Attacks unlike the original, where he only thinks of the Cyclone Bros. attack.
 * Mario's and Luigi's HP and BP are no longer fully refilled after defeating bosses.
 * The Super version of the Thunder Bros. features a purple electrifying uppercut with three lightning bolts instead of blue with one lightning bolt if Luigi executed it correctly.

Puzzles and minigames

 * The time limit to collect ten Hoohoo Spirits in Hoohooros's minigame has increased from 30 seconds to 35.
 * The amount of Hee Beans rewarded from mini-games have been altered slightly. Some minigames have their point goals lowered to make earning Hee Beans easier.
 * The amount of blocks needed to be hit in Jojora's block minigame in Joke's End has decreased from 30 to 25.

Characters

 * Many character sprites are derived from the sprites of Mario & Luigi: Dream Team and Mario & Luigi: Paper Jam, causing their appearance to be different with respect to the one of the original game.
 * Troopeas are bipedal rather than quadrupedal, wearing shoes and otherwise more closely resembling their Koopa Troopa counterparts, apart from the beansprouts on their heads.
 * The Koopalings take on their modern designs rather than their original designs.
 * The NPC Koopa Troopas from the Koopa Cruiser no longer wear flight uniforms.
 * The Toads in Peach's Castle and Little Fungitown are now regular Toads with differently colored spots and vests rather than differing in height and clothing.
 * The large, pudgy Ankoopas that block paths have been replaced with larger, ordinary Big Koopa Troopas.
 * Mechakoopas replace Mecha-Chomps in Woohoo Hooniversity.
 * Dr. Toadley replaces Psycho Kamek in Little Fungitown.
 * The top faces of Oucher Glasses appear to have happy faces rather than sad ones, while the mad faces on the bottom stay the same.
 * Bink's design has been changed from his original Donkey Kong-like appearance to that of a generic S.S. Chuckola crew member.
 * Boomerang Bros. from the original game are now named Beanerang Bros. and are treated as a separate race to the standard Mushroom Kingdom ones (which are found in Minion Quest). They also drop Oho Gear in all versions.
 * Cheep Cheeps and Puffer-Cheeps are replaced by Spiny Cheep Cheeps with the same behavior.
 * Several enemies that had duplicate names but different palettes and stats have been renamed to be "Elite" versions, akin to what Elite Troopea was to Troopea. These include Elite Pestnut, Elite Chuck Guy, Elite Gritty Goomba, Elite Dry Bones, and Elite Limbo Bro.
 * Cackletta's soul has been given a new design. She has a blue jewel on her forehead, has light yellow eyes instead of darker yellow, bloodshot ones, and her arms are now color coded to match the elements they use. Additionally, she is bigger and is a 3D model rather than a 2D sprite (as with Shiny RoboBowser).
 * When low on health Cackletta's entire body gains a red tint, the eyes and heart turn green, and the jewel becomes gray.
 * Cackletta raises her index finger rather than her middle finger when using her spinning fire attack.

Areas

 * Toadtown Square was renamed "Peach's Castle".
 * Beanbean Outskirts was renamed "Beanbean Fields".
 * Beanbean Castle Sewers was renamed "Beanbean Castle Sewer".
 * Four new green pipes were added, bringing the total amount from nine to thirteen: one in Hoohoo Village, one at the Mine Cart Platform at Hoohoo Mountain Base, one in Chucklehuck Woods near Winkle Colosseum, and one at the start of the surfing minigame in Oho Ocean.
 * Because the player has access to the map on the touchscreen, maps on the walls of areas no longer appear.
 * There are now ? Blocks in the game that contain soundtracks that are added to the Music player.
 * Beanbean troops now block the pathways to the north and south Beanbean Fields until the player defeats Queen Bean.
 * Invisible beanholes that can be found by Mini-Mario or the Game Boy Player are now made visible.
 * The Magikoopa in the second room of Bowser's Castle is no longer seen.

Music

 * Various music has been replaced. The music for the Star 'Stache Smash has been replaced with an arrangement of Mario & Luigi: Paper Jams mini-game theme, the music for the Barrel and Chuckola Bounce mini-games is replaced with an arrangement of Mario & Luigi: Dream Teams mini-game theme and the tutorial music is an arrangement of Mario & Luigi: Partners in Time's tutorial music.
 * When getting a game over, an arrangement of the death jingle from Super Mario Bros. can be heard, while in the original game, the battle music continues playing.
 * In the opening scene, Prince Peasley's full theme plays before Fawful steals Princess Peach's voice. In the original game, a drumbeat is heard before the first half of Prince Peasley's theme plays.
 * Instead of the music stopping when Peach's Castle explodes, the music keeps playing as it explodes.
 * After landing in Stardust Fields, the music does not start playing until after the cutscene where Luigi gets stuck in the ground is over.
 * The music no longer changes during the scene where Dragohoho hatches from his egg; instead, the Hoohoo Mountain theme keeps playing until the boss battle starts.
 * When Mario & Luigi enter Beanbean Castle during both times the town is under attack, the devastation theme keeps playing instead of the Beanbean Castle theme.
 * Professor E. Gadd's theme is now taken from Luigi's Mansion: Dark Moon rather than being an arrangement of his theme from the original game.
 * Sledge and Mallet's cave home in Beanbean Fields now plays the Beanbean Fields theme instead of the Hoohoo Village/Beanbean Castle Town theme.
 * Rather than the music for Gwarhar Lagoon/Oho Oasis playing after the S.S. Chuckola moves out of Teehee Valley and into the ocean and crashes, no music plays.
 * When Mario confronts Bowletta and Fawful on top of Joke's End, Cackletta's theme plays instead of the Joke's End theme.
 * The danger music plays when Larry traps Luigi in a barrel; in the original game, the danger music does not play.
 * The battle music that was used for Fawful in Bowser's Castle is now the battle music that was used for Cackletta in Woohoo Hooniversity just like in the original game's Japanese release, rather than that used for Popple as in the original game's releases outside of Japan.
 * Before Mario and Luigi fight against Bowletta, Cackletta's theme does not speed up like in the original game.
 * In the original game, when Bowletta pretends to be defeated, the devastation theme plays, then the music stops when the Time Bob-omb arrives. After it KOs Mario and Luigi, Cackletta's theme plays as Bowletta gloats over the brothers lowering their guard before she inhales them.  In the remake, Bowletta's boss music continues until the brothers have been inhaled, though it still stops as normal before resuming.

Miscellaneous

 * The "M" and "L" on Mario and Luigi's respective caps are now red and green respectively, instead of both being black.
 * Mario & Luigi now make sounds whenever they are hit in battle as well as during Bros. Attacks.
 * The level of an enemy is now displayed next to their name when targeting them in battle.
 * The Toads guarding Princess Peach no longer abandon her in Cackletta's attack, but are struck down by lightning.
 * Several cameos have been added to Mario's House:
 * There is now a trophy from Mario Kart 8 on a shelf and a Wii Wheel hanging next to it.
 * Mario's tennis racket and golf club can be seen on a shelf above and leaning on Mario's bed, respectively.
 * Mario's hardhat and tool belt from Super Mario Maker is hanging beside the workbench on the first floor of Mario's House.
 * Mario's Cap is now on the clothing line outside of the house rather than on the coat-stand inside, fixing a minor continuity issue when Mario puts on his clothes.
 * A carpet in front of the Bros.' beds looking like a Yoshi's Egg has been added.
 * Mario's yellow cape from the Cape Mario form can be seen on the coat hanger.
 * Above the stairs, there is a picture of a Shroob saucer.
 * A pendulum clock has been added to the wall.
 * A blueprint of the first level in Mario Bros. can be seen on the workbench.
 * Mario does not jump on the Toad that tells him about Peach.
 * Each area has a unique stamp when the game is saved, whereas in the original, there was only one stamp. For example, Peach's Castle has a mushroom stamp whereas the Koopa Cruiser and Bowser's Castle have Bowser's head as a stamp.
 * After Tolstar tricks Bowser after giving him 100 coins, Bowser calls him a "swindler" rather than a "welcher." This may have been changed because the older term is offensive slang in the United Kingdom.
 * The cannon that Bowser gets stuck in during Stardust Fields now flies away upon firing him out, rather than blinking away after the camera pans back to Mario and Luigi.
 * After Mario and Luigi leave Beanbean Castle after beating Queen Bean, a Pea shows up and gives Mario a badge and teaches him how to equip badges with Luigi sulking over not getting one like in the GBA version. However, badges drop as early as the Tolstar battle in this version.
 * During Popple and Rookie's battle in Chateau de Chucklehuck, if Popple has been damaged for the first time, Rookie calls him "Boss" rather than "The Great Popple". This was likely done to keep Rookie's dialogue consistent.
 * The Starbeans Cafe clerk no longer asks the player if they wish to continue making more drinks after making one.
 * Bean depressions are now known as bean hollows.
 * Dr. Mario sound effects are added when fighting Viruses in Woohoo Hooniversity.
 * Sledge and Mallet now inform Mario and Luigi that they've moved after defeating Mom Piranha and tell them to come by.
 * They are also not in the cave until then. In the original, they could be visited any time after Oho Oasis.
 * Geno no longer explains the minigame, Star 'Stache Smash, with a disembodied text bubble replacing him. This is likely due to licensing reasons, as Square Enix owns the character of Geno.
 * The monitor that Bowletta uses to communicate with the heroes in Beanbean Castle is now a Nintendo 3DS (blue the first time and pink the second time), rather than the original game's Game Boy Advance.
 * The original map of the Beanbean Kingdom from the original version of this game can be found in the captain's quarters of the S.S. Chuckola.
 * The underwater sections in Gwarhar Lagoon have a greener tint and a slightly different battle background from the sections in the Seabed.
 * One of the two Toads that was convinced into winning an Invincibility Mushroom now wonders if it might pump up his muscles rather than the possibilities of clearing up his skin.
 * When Mario gains Bean Fever, while in this state, his HP is reduced to 1 and his BP is reduced to 0, but when he is cured by the Crabbie Grass, his HP and BP will be full.
 * The underground sections in Teehee Valley use the same battle background from the Guffawha Ruins.
 * The posters in Yoshi Theater, which used to reference other Nintendo franchises such as Kirby, Wario, and The Legendary Starfy, are now replaced with new posters depicting films mostly involving characters from previous Mario & Luigi games, including Broque Monsieur, Broque Madame, and Broggy (Bowser's Inside Story), a Shroob invasion (Partners in Time), Prince Dreambert (Dream Team), and a Cheep Cheep.
 * There is now a night sky in Joke's End when climbing up to the fourth and fifth floors.
 * When Prince Peasley informs Queen Bean that the civilians of Beanbean Castle Town have been evacuated, he now flourishes his hair with a gleam.
 * The original game featured a cutscene upon entering Bowser's Castle, where Fawful informs Bowletta about the arrival of Mario and Luigi, and she summons the Koopalings. This cutscene is missing from this game, since in Minion Quest, Bowletta disguised as Bowser orders Captain Goomba and the other minions of Bowser to attack Mario and Luigi instead.
 * The Koopalings are now given a full amount of dialogue since they do not have any in the original game.
 * The mini Mechakoopas in Ludwig's section of Bowser's Castle have been replaced with purple versions of the windup toys in Woohoo Hooniversity.
 * Roy Koopa now explains the Time Bob-omb's function instead of an on-screen text.
 * The ground during the final battle now has a design of Cackletta's grin.
 * Bowser's reaction upon it being revealed that he was in fact Peasley's "gift" varied from the original game. Originally, he was shown sneezing (implying that he caught a cold presumably from his fall into the ocean earlier). Now, he is shown sobbing before proceeding to rage out, implying that he was not fond of being stuck inside the package.
 * The credits now show the plane's destination from behind. Originally, they were shown to the side of the plane. As such, when it passes over Bowser's Castle, Bowser just falls off-screen. In Minion's Quest, it was revealed that his castle was destroyed after the present fell off. It was later rebuilt by his minions after the destruction.
 * Additionally, when the words "THE END" appear, the Yoshis no longer applaud; instead, the screen fades to black. The Yoshis applaud in the title screen instead for the 3DS remake.
 * Fawful no longer misspells Cackletta's name as "Cakletta" when he mentions her before he fights Mario and Luigi a second time. Additionally, Peach's line "Wow! Luigi! You're face looks so much more...manly!" has been changed to "Wow! Luigi! Your face looks so much more...manly!" due to the original quote having a typo.

Enemies
Regular enemies Bosses

Minion Quest: The Search for Bowser
This adventure exclusive to this remake develops alongside and with the main Mario Bros. story. It involves Bowser's minions battling the enemies of the Beanbean Kingdom to rescue Bowser, after he is knocked out from the Beanbean Border, led by Captain Goomba. The battles are the two armies automatically fighting against each other, though the player can choose which characters to send in, give more power to Special Skills by performing certain actions such as repeatedly pressing a button, pressing a button with the correct timing or aiming correctly at the enemies, and choose one of the actions available to the captain, the latter of which costs CP. At the end of a battle, there's a chance of one or more of the opponent's allies joining the player's team. There are three types of troopers: Melee (who only fight physically), Ranged (who fight exclusively with projectiles), and Flying (physical fighters who fly). The types follow a rock-paper-scissors triangle of strength and weakness, with Melee units being strong against Ranged units but weak against Flying units, Ranged units being strong against Flying units, but weak against Melee units and Flying units being strong against Melee units but weak against Ranged units.

Story
The story of Minion Quest is shown as a movie, just like the main Mario Bros. story, in the Yoshi Theater.

The story starts off right after the Mario Bros. have defeated the first two enemies in the game, the two Goombas. After they are defeated, they are placed in barrels, and the one on the right complains about how he got trounced by the Mario Bros. again, with the one on the left saying that it's about time the Goombas rose up and made a name for themselves. Unbeknownst to anyone in Bowser's army, these two Goombas would eventually become Captain Goomba and Private Goomp over the course of their adventure.

They are taken care of by the Koopalings Roy, Wendy, and Iggy, who tear into them and mercilessly taunt them about how useless, expendable, and trash they are and proceed to give them orders, but before they can do so, the Koopa Cruiser gets attacked by Fawful and starts to sink into the area around the border between the Mushroom and Beanbean Kingdoms, just like in the main story, and every one of Bowser's army of baddies is thrown clear of the wreckage.

Captain Goomba regains his consciousness and awakes in a cave. He attempts to see if there is anyone nearby, but he can hear no answer, so he looks outside and finds that he is on a huge mountain. He sees Bowser, who had just been shot out of the cannon in Stardust Fields, fly through the air into the distance. Deciding to rush after his leader, the captain of the Goombas warms up for some action and takes off in pursuit of Bowser, and thus begins the untold adventure. After beating two Beanies who come across his path, Captain Goomba comes across some of his fellow kind arguing over who should be the captain and lead the rescue. Overcome with joy, he meets up with them, where they explain the situation to him, and after he convinces them to join him on the adventure, they officially make him a captain and give him his flag. Initially they only agreed to this because no one else wanted to, but he slowly starts to win their sincere support and respect and prove himself a true captain. Captain Goomba learns the tutorials of the game the first few levels.

The crew fights various Goombas, and a pair of Hammer Bros. who were going to live with the Hammerhead Bros. The squad comes across two Paragoombas, who take Captain Goomba for an enemy and attack his squad. After defeating them, the now-freed Paragoombas tell him the bad news: Fawful came across Bowser and made plans for him, and the Paragoombas attempted to interfere and stop him, but he brainwashed them with his headgear's smoke and shooed them away to fight his enemies. The minions make fun of the captain's "aura of stupidity"; this becomes a running gag throughout the story. Ludwig and Lemmy are encountered on the mountain, but they pay the squad no mind as they continue to look for Bowser themselves.

Eventually, Captain Goomba comes across Fawful, who has Bowser with him. Before he can do anything, however, Private Goomp arrives to take credit for defeating Fawful. Fawful uses his brainwashing smoke to brainwash Private Goomp, but fails to brainwash Captain Goomba due to his true minion spirit. Captain Goomba and his squad fight against Private Goomp and his brainwashed forces, and after the battle, Fawful knocks Goomp and Captain Goomba off the top of the mountain, and flees to the castle to retrieve the Beanstar, once again drawing parallels with the main story. Later, Captain Goomba consults a Hoohooligan about Bowser's whereabouts, and jumps off the bridge to the base of the mountain, making a huge crash in the process.

Outside Beanbean Castle Town, the Koopalings are discussing their plans about how to find Lord Bowser, and even wonder if he has been kidnapped. They easily dispatch a rowdy group of Beanies, but are ambushed by Fawful, who uses a more powerful spray to brainwash all the Koopalings after the normal one proved to be ineffective.

Captain Goomba and his squad come across a Shy Guy strolling around, who throws a turnip at Goomba. Afraid for a second that he might be brainwashed, the captain is ready to fight, but the Shy Guy says they are on the same side, and he was only attacking due to the fact other minions were hostile. Shy Guy joins Goomba's team as a new captain.

The two captains and their squad eventually encounter Lakitu, who explains to them that when the Koopa Cruiser exploded, it sent the minions flying across the entire kingdom, and that they will have to recruit all of the minions before taking their last stand against Fawful. Lakitu says he will scout the nearby areas for any minions, but before he can do so, a brainwashed Larry snatches him away for building Fawful's army. However, the duo of captains are able to rescue him, and they continue their search.

Later on, the group runs into Prince Peasley, and they ask him if he has seen any Stalking Piranha Plants lately. One sneaks up behind Captain Goomba, and a battle ensues with a few Piranha Beans. After the fight, Captain Goomba humorously sends a Piranha Bean to attack Prince Peasley. The squad then encounters the Elite Trio, with Private Goomp at the forefront. Goomp says he intends to recruit all the minions and get recognition from Bowser, so he, along with Sergeant Guy and Corporal Paraplonk, fight the squad, with Captain Goomba winning the battle. After the battle, the three then argue over why they lost, causing a fight to ensue. The squad decides to ignore them and continue. Eventually, the group confronts Larry, who is ordering his minions to help build a fortress for him, so he can conquer Beanbean Castle Town. In the ensuing battle, Captain Goomba wins against Larry, and convinces him to join their cause, although Larry strongly dislikes taking orders from a Goomba. He informs the squad that the Koopalings are scattered around the world, knowing the locations of three of the Koopalings: Iggy in Chucklehuck Woods, Wendy in Gwarhar Lagoon, and Morton in Teehee Valley.

The squad enters a cave filled with Boos, and encounter Professor E. Gadd, who talks about his ghost research and his inventions, including a time machine. They wander into Chucklehuck Woods, where Iggy is busy taking over the forest. Captain Goomba starts to smell an addictive fragrance that makes him wander off into Bubbles' lair. Inside the cave, they see Bubbles, who mistakes them for the ones who are causing the turmoil in the forest, and he breaks the floor with his feet, sending the entire squad plummeting down into the underground. Getting out, they encounter Cork and Cask, who ask for help retrieving the Red Goblet in exchange for info on Iggy's whereabouts. Sergeant Guy has split up with the Trio, and attempts to beat the squad alone, but fails and instead joins the squad. The squad soon meets a Boo who becomes another captain (although he just wanted the flag). Finally, at Mother Chuckalola, the squad encounters and defeats Iggy, and he joins the squad's team.

In Gwarhar Lagoon, Captain Goomba is swarmed by eager Hermie club fans, only for Wendy to appear and taunt the squad. The Hermie club then attacks Wendy, so the minions give chase. Although she escapes, she has set up a "cute battle contest" that will determine the cutest group, which the Hermie club plans to join. Hermie III snatches a Bob-omb and Starlow, a Star Sprite, to use as decorations for the cute contest, which leaves the rocking starfish Spangle dejected. Starlow escapes, and shooes both Hermie and Spangle away, before leaving to possibly enter the cute battle herself. Corporal Paraplonk is encountered training his Paratroopas for the contest, and after a battle, joins the squad. The cutie battle begins which gives Shy Guy stage fright, and he bails as a result. The minions must get through a few rounds earning points, and eventually Wendy gets fed up and decides to fight early. After the battle, Wendy joins the squad, and after leaving, the Star Angels (Starlow, Spangle, and two Starkisses) end up winning the prize.

Back at Hoohoo Mountain, Bowser is seen looking for food. The minions lose sight of him, and ask a Hoohooligan what happened to Bowser. He explains that Bowser was able to escape Fawful's capturing, but got struck by a "hard object" (which made him lose his memory). Popple, who was in the village stealing food, trips on Bowser, causing him to wake up and start following Popple. Back at Chucklehuck Woods, Popple has already made Bowser his Rookie, but momentarily loses sight of him. Popple asks the captains for help in finding "Rookie," but they intimidate Popple into fighting. Rookie does appear, however, but he does not recognize his former lackeys, and burns Captain Goomba when the latter tries constantly to no end to get him to come back home to the castle before leaving.

The squad makes their approach to Teehee Valley, where Morton is attempting to take over the Toad village. Encountering Private Goomp in the desert, they battle his Goomba squadron and gain him as the last Elite Trio member. They "save" a single Toad that works at the arcade at the town, and bribes Captain Goomba into getting an Invincibility Mushroom in a cave in exchange for beans, and in yet another parallel to the main story, it turns out they got a Poison Mushroom instead of an Invincibility Mushroom, which caused Mario to get Bean Fever. Among a group of Troopeas, a lone friendly Koopa is encountered, and becomes a captain, though his affinity for rhyming is usually frowned upon. Eventually, the group finds Morton and defeat him, and he joins the squad.

Popple is encountered again, this time looking for a replacement for the previous Rookie (candidates include a Fighter Fly, a Beanie, a Paratroopea, a Tanoomba, and Birdo). Upset that the squad attacked him in the Woods, Popple fights the minions, but is defeated again. Birdo, the only Rookie left, carries Popple away. Meanwhile, the cutscene where Bowser becomes Bowletta plays, implying Bowser was just beaten.

Lakitu informs the crew that the Koopa Cruiser is being repaired in Joke's End, but Fawful appears to tell them he took over Bowser's Castle, and that Bowser is "no longer of this world anymore." Making their way to Joke's End, they find the Koopa Cruiser in ruins, so they decide to defeat minions to gather tools, unaware they are being spied on by Roy. Once they have enough allies, Roy launches a surprise attack, but soon comes to his senses and joins the squad, telling the squad to stop a bomb the Elite Trio had placed on the cruiser. With the cruiser repaired, the squad flies to Bowser's castle.

The castle is filled with the hardest enemies thus far. Ludwig and Lemmy are encountered and fought, and once defeated, the Koopaling team is complete. Eventually, as a test of strength, Ludwig orders all the Koopalings to fight at the same time. Captain Goomba defeats them all, and they gain the Koopalings' respect.

The group encounters Fawful once again, and although he taunts the squad mercilessly, they defeat him and make their way to Bowser's chamber, where Bowser (seemingly returned), immediately tells Captain Goomba to "destroy" Mario; it is presumed that the army turns its attention to the Mario Bros after this. After a while, it turns out "Bowser" was actually Bowletta in disguise, and when Captain Goomba confronts them about this, she and Fawful use a trapdoor to send the squad into a dungeon, which turns out to be a Mecha-Fawful factory. After a long final battle which tests all the skill levels, the minions defeat Fawful one final time and escape the dungeon. It is unknown what happened to Fawful after this, it is presumed he fled and went on to fight Mario and Luigi, once again in a parallel to the main story.

After Bowletta's ultimate defeat, the minions reunite with a returned Bowser, only for the castle to explode sending Bowser and his minions crashing into the screen. Later, Bowser gets stuck in the present in the airplane, and all the minions chase after it on their way home. Back at Bowser's castle, Bowser begins to promote Captain Goomba, only to realize he was the "hard object" that fell on Bowser's head and gave him amnesia. Bowser angrily chases after Captain Goomba, and his title and flag are taken away as the story comes to a close.

CP
CP are used to activate Captain Commands. The higher the captain's level is, the more CP and Captain Commands he will have; each captain can have a maximum of 10 CP. After a battle, some CP is restored; by 1 if the captain has a maximum of 1-5 CP, 2 if the captain has a maximum of 6-8 CP, and 3 if the captain has a maximum of 9 or 10 CP. The only other way to increase CP in a level is through the Chance Captain Command; if the player is lucky, they will get 5 CP out of it, but it costs 3 CP to use.

Other characters

 * Hammerhead Bros.
 * Bowser
 * Professor E. Gadd
 * Cork and Cask
 * Rookie
 * Hermie III
 * Spangle
 * Toad
 * Bowletta

amiibo support
The game is compatible with the following amiibo from the Super Mario series.

amiibo can be used after the player defeats Queen Bean and grants stamps which can be redeemed for prizes.
 * Mario
 * Luigi
 * Peach
 * Yoshi
 * Toad
 * Bowser
 * Bowser Jr.
 * Boo (read/write)
 * Goomba (read/write)
 * Koopa Troopa (read/write)

Nintendo eShop description
''There are so many surprises, thrills, and laughs in store for Mario and Luigi that it isn't even funny...except it is! Every hoo-hoo, hee-hee, and ha-ha in this classic RPG adventure has been remade for Nintendo 3DS™ systems. Plus, an all-new squad-based strategy tie-in sees Bowser's Minions on a quest to stop Fawful. "Have you readiness for this?!?"''
 * American version

''Sure you do! So guide the Bros. on a journey through the Beanbean Kingdom to recover the stolen voice of Princess Peach. Every step on your path and every stomp on a Goomba has been completely recreated with enhanced graphics, lighting, and new gameplay options. Take down enemies using special Bros. Attacks and solve puzzles with Bros. Actions. Do you have fury? Especially due to Fawful? Then go behind the scenes of this superstar saga by captaining an army of Bowser's minions. With 50+ minions to recruit, strategy is on your side!'' ''The game that launched the Mario & Luigi series returns looking better than ever before. In this renewed classic, Mario and Luigi journey to the Beanbean Kingdom with Bowser to restore Princess Peach's voice.''
 * European/Australian version

''Control Mario and Luigi simultaneously, making use of their unique Bros. Moves to solve puzzles and emerge victorious in action-packed battles. Pay heed to the enemy's patterns and time your reactions right to land satisfying counterblows.''

''Included in this remake is the Minion Quest: The Search for Bowser mode, which tells the story of the game from the perspective of Bowser's minions. Recruit characters to grow you own Minion army as you fight to locate your missing leader!''

Wrong Action Commands
If the player flees a battle, remains touching the enemy, and initiates a Dunk Hammer at the same moment the enemy finishes blinking, the battle will begin with Mario's hammer in the air. If the player flees again, Mario will remain in the back regardless of what command is selected, and can use Luigi's commands with various odd results. Entering a Green Pipe while this glitch is in effect will disable all action commands. The game will softlock if either Mario or Luigi hits a Heart Block.

Promotion
A quiz game, Mario & Luigi: Superstar Saga + Bowser's Minions Trivia, was released on the Play Nintendo website in 2017.

Staff
The remake was directed by Shunsuke Kobayashi and produced by Shinya Takahashi and Tetsuo Mizuno, with Shigeru Miyamoto and Takashi Tezuka supervising the production. The arrangements of the music cues in the game were written by Yoko Shimomura, the same person who composed the tracks originally.

Unused Beanbean Kingdom image
An unused, higher-resolution version of the Beanbean Kingdom background from the title screen can be extracted from the game's files. The image is never fully seen in-game, as it is partially covered by clouds and the edges are cropped.

Captain Beanie
A Beanie with a blue flag, which appears to be incomplete due to the flag not animating, exists in the game's data. It may have been an early idea for how enemy captains would look before they were made to look the same as other enemies.

References to other games

 * Super Mario Bros.: An arrangement of this game's death jingle is heard when getting a game over.
 * Super Mario Bros. 3: The Koopalings reprise their roles from Superstar Saga. They also appear in the Minion Quest side-mode, where Larry is the boss of the plains world, Morton is the boss of the desert world, and Wendy is the boss of the water world, as they were in this game.
 * Mario Golf series / Mario Tennis series: Mario's golf club and tennis racket can be seen next to his bed.
 * Paper Mario series: The Goombas' Rocket Headbutt Special Skill in Minion Quest is similar to their Headbonk move from these games, along with the Headbonk Goombas from Super Paper Mario.
 * Luigi's Mansion: Aside from the reference supplied when encountering him in the main game, E. Gadd also mentions that he created the Starbeans Cafe franchise to provide funding for his ghost research during the events of Luigi's Mansion when encountering him in Minion Quest.
 * Mario & Luigi: Partners in Time: A poster depicting a movie involving a Shroob invasion appears in the redesigned Yoshi Theater. E. Gadd also mentions he is building a time machine when encountered in Minion Quest. A picture of a Shroob saucer is seen in Mario's House above the stairs.
 * Super Mario Galaxy / Super Mario Galaxy 2: Bomb Boos appear in Minion Quest.
 * Mario Kart Wii: A Wii Wheel is shown under the stairs in Mario's House.
 * Mario & Luigi: Bowser's Inside Story: Dr. Toadley replaces Psycho Kamek, while Broque Monsieur, Broque Madame, and Broggy cameo on another poster. Starlow and Mechawfuls also appear in Minion Quest.
 * Luigi's Mansion: Dark Moon: E. Gadd's theme is directly taken from this game.
 * Mario & Luigi: Dream Team: The game runs on the same engine used in this game. Many graphics originate in this game. Prince Dreambert also cameos on a poster. One minigame theme in Mario & Luigi: Superstar Saga + Bowser's Minions is an arrangement of "Challenging Actions" from Mario & Luigi: Dream Team.
 * Mario Kart 8: A trophy from this game appears in Mario's House.
 * Captain Toad: Treasure Tracker: An Invincibility Mushroom appears in Minion Quest.
 * Super Mario Maker: Parts of Mario's Builder Outfit, specifically the hardhat and toolbelt, appear in Mario's House.
 * Mario & Luigi: Paper Jam: An arrangement of "Do It Now!" appears as a minigame theme in this game.
 * Paper Mario: Color Splash: Morton's way of speaking is similar to how he speaks in this game.

References in later games

 * Super Smash Bros. Ultimate: The battle theme in Minion Quest: The Search for Bowser appears as music in this game.
 * Mario & Luigi: Bowser's Inside Story + Bowser Jr.'s Journey: The Minion Quest mechanic returns as a story mode for Bowser Jr. In addition, Captain Goomba, Captain Koopa Troopa, Captain Boo, and Captain Shy Guy make a reappearance as enemies and allies. Captain Goomba's inadvertent role in giving Bowser amnesia (as well as that mode's ending where he got demoted as a result) is indirectly referenced right before Bowser Jr.'s tutorial fight against him, where Captain Goomba states he does not wish to upset Bowser again. Both Morton and Ludwig also reference the Captains' role in saving Bowser near the beginning of and late in the game, respectively.