Mario & Luigi: Bowser's Inside Story + Bowser Jr.'s Journey

Mario & Luigi: Bowser's Inside Story + Bowser Jr.'s Journey (known as Mario & Luigi RPG3 DX in Japanese) is a game for the Nintendo 3DS. It is an enhanced remake of the 2009 Nintendo DS game Mario & Luigi: Bowser's Inside Story. The remake also features another story where Bowser Jr. takes action on an adventure, similar to Minion Quest: The Search for Bowser, with two important differences: a slot for an additional first officer who will have its own actions just like Bowser Jr. as well as formations for the troops.

The game is the second enhanced remake of the Mario & Luigi series, the fourth game in the series to be released for the Nintendo 3DS, and the seventh game in the series overall, as well as the thirty-first Mario game released for the Nintendo 3DS. It is also the final Mario & Luigi game released by AlphaDream before filing for bankruptcy.

The game is now amiibo compatible: scanning one will grant the player an item. According to the manual, the same amiibo can only be scanned once per day.

General

 * The game now has an additional game mode, Bowser Jr.'s Journey, which can be played at any time from the start of the game.
 * The game no longer makes use of the Mic feature. As such, the Mic Test no longer appears on the title screen.
 * The game is now amiibo-compatible, and an amiibo can be scanned once a day to grant the player an item.
 * Some practices from the original game do not reappear. This is likely due to the Battle Guide.
 * The button can now be used to fast-forward cutscenes.
 * When adventuring as the bros., the button can be pressed to jump at the same time, or to swim simultaneously while in Pump Works.
 * Likewise, switching from the Bros. to Bowser can now only be performed by pressing instead of either  or.
 * A map icon in the bottom right corner allows Bowser or the bros. to see a map of their current location.
 * Toad Square now announces more items and gear are in stock in the shop and occasionally makes a sale on Emoglobin Juice throughout the game.
 * Some Gear and Accessory locations have been changed.
 * Badges now have the same names and similar effects as those from Mario & Luigi: Dream Team.
 * The Bros. now need to continue the story to unlock more badges in the badge store.
 * Likewise, when the Bros. reach Rainbow Rank, they do not get Luigi's final badge; instead, they now need to get a gold rank in all Cholesteroad challenges in the Challenge Node to obtain his final badge.
 * The "Easy" mode for Bros. Attacks returns from Mario & Luigi: Superstar Saga + Bowser's Minions.
 * Mario, Luigi, and Bowser now start with three Gear slots by default.
 * Like in Mario & Luigi: Dream Team, the player can hold more than one badge at a time.
 * Unlike in Mario & Luigi: Dream Team, the badge meter does not increase when having two badge effects in stock. One of them must be used to put another badge effect in place.
 * There are now two extra Badges for Mario to use.
 * The Silver Badge is received after getting all 16 Mushroom Balls in Toad Town, and the Expert Badge is received by defeating Bowser Memory MLX in The Gauntlet.
 * Scratch Cards (now known as "Bonus Cards") are now played by choosing a square with the and buttons.
 * Enemy stats have been changed.
 * Some bean locations have been changed or altered.
 * When Mario and Luigi are using the Breath Inspector in Dr. Toadley's office, it is now performed by pressing the and  buttons respectively instead of blowing into the mic.
 * Kuzzle now gives five of every type of bean instead of ten after completing all puzzles. He also gives the player a Barrier Wear.
 * Bowser can no longer punch the Boo-ray Machine; instead, he must stand on the pad to activate the spotlight.

Battles

 * Mario and Luigi can now activate Emergency Guard by holding.
 * Like in Mario & Luigi: Superstar Saga + Bowser's Minions, landing a First Strike on an enemy with a Hammer will give them a SPD-Down effect.
 * Like in the other 3DS Mario & Luigi games, the hammer can be held for an infinite amount of time, making defending attacks with hammers easier.
 * Like in Mario & Luigi: Dream Team, Fleeing will not cause the player to lose coins.
 * The Battle Guide now takes the form of a Command Block called the "Guide Block" for both the Bros. and Bowser during battles.
 * The maximum number of hits of Bowser's Fire Breath attack has been reduced from five hits to three hits.
 * The Badge Command Block to change badges during battle is absent from the remake; instead, they are changed at the bottom right corner on the touch screen.
 * Super Bowser has a new attack as a finishing move during giant battles called "Spinning Slide", which involves drawing a circle with the stylus similar to Mario & Luigi: Dream Team.
 * Spinning Slide also appears when Super Peach's Castle of Fury attacks to let the player spin Bowser.
 * Super Bowser's Fire Breath attack is now done by tapping the touch screen instead of blowing into the mic.
 * Bowser can now attack enemies to make them drop Blitties so he can inhale them.
 * Experience Points are no longer received from giant battles; instead, items and gear are rewarded like giant battles in Mario & Luigi: Dream Team and papercraft battles in Mario & Luigi: Paper Jam.
 * Changing Badges no longer takes up a turn.
 * Giant battles can now be re-fought in The Gauntlet.
 * Chain Chawful now takes damage from Bowser's shell. It also rewards 25 experience points if defeated by inhaling the Sworm.
 * Broque Monsieur no longer takes damage during a battle tutorial if the player refuses to learn how to use the Vacuum Block. As such, the battle will only end if the player inhales him to continue the story.
 * The player can now help Luigi escape Junker and Junker X's suction that puts him in a Junker Can and Junker Can X respectively by mashing the button.
 * When defending against Super Bowser X's Fire Breath attack, the player must hammer the fireballs away instead of jumping over them.
 * When Bowser (during his second fight) and Bowser X get angry, he will fully heal himself with a Drumstick.
 * Mario and Luigi can no longer hold onto Starlow indefinitely after avoiding Bowser's and Bowser X's flame or the Dark Star Core's huge beam, and will automatically drop down after the attack ends. They must still let go themselves after the Dark Star's beam however, due to avoiding its ramming attack that follows.

Ranks

 * Rank-Up Bonuses return from Mario & Luigi: Dream Team and Mario & Luigi: Paper Jam.
 * The Boomerang Rank from Mario & Luigi: Paper Jam returns for Mario and Luigi. Said rank replaces the Shine Rank and switches places with the Flower Rank.
 * Bowser's "Final Boss" rank is retooled as his fifth rank, while receiving a new fourth rank: Master Boss.

Bros. Attacks

 * Mario and Luigi's Special Attacks are renamed Bros. Attacks and now cost different amounts of BP:
 * The Green Shell Bros. Attack now costs 4 BP instead of 3 SP.
 * The Fire Flower Bros. Attack now costs 6 BP instead of 4 SP.
 * The Jump Helmet Bros. Attack now costs 10 BP instead of 6 SP.
 * The Yoo Who Cannon Bros. Attack now costs 14 BP instead of 7 SP.
 * The Super Bouncer Bros. Attack now costs 12 BP instead of 7 SP.
 * The Spin Pipe Bros. Attack now costs 16 BP instead of 10 SP.
 * The Mighty Meteor Bros. Attack now costs 20 BP instead of 8 SP.
 * The Snack Basket Bros. Attack now costs 18 BP instead of 14 SP.
 * The Magic Window Bros. Attack now costs 26 BP instead of 18 SP.
 * The Falling Star Bros. Attack now costs 28 BP instead of 20 SP.
 * The number of hits of the Green Shell Bros. Attacks for the Bros. has been reduced from ten hits to six hits, and the finishing attack is similar to the 3D Red Shell and 3D Green Shell from Mario & Luigi: Dream Team and the 3D Red Shell from Mario & Luigi: Paper Jam.
 * Spin Pipe has been shortened so that the player must tap the appropriate button in a rhythmic fashion, followed by a single long rotation.
 * The number of hits of the Mighty Meteor Bros. Attack for the Bros. has been reduced from five hits to four hits.
 * Magic Window has been nerfed and no longer uses infinite inputs; the attack now ends with three windows on both sides opening one by one, with both bros jumping out of them to stomp on the enemy.
 * The Fire Flower Bros. Attack no longer damages Calorites, but heals them instead.
 * Yoo Who Cannons now aim at the enemy while the attack is in use.

Brawl Attacks

 * Bowser's Special Attacks are renamed Brawl Attacks and now cost different amounts of BP (with the exception of Goomba Storm and Shy Guy Squad):
 * Koopa Corps now costs 14 BP instead of 10 SP.
 * Bob-omb Blitz now costs 18 BP instead of 12 SP.
 * Magikoopa Mob now costs 24 BP instead of 15 SP.
 * Broggy Bonker now costs 28 BP instead of 20 SP.
 * The Shy Guy Squad Brawl Attack can no longer slide with the styles indefinitely; instead, the attack stops after the Shy Guys push Bowser three times if the player slides the stylus to get an "Excellent".

Items

 * Bowser now eats Cheese instead of Syrup Jars to restore BP.
 * Likewise, Bowser now eats Cheesy Drumsticks instead of Star Candies to fully restore his HP and BP.
 * Defense Beans, Speed Beans and Flex Beans now appear in the game.
 * Retry Clocks no longer appear like they do in the original version, as the player can retry a battle at any time (or in Easy Mode) if the player gets a Game Over like in the other 3DS Mario & Luigi games.
 * Boo Biscuits now appear as items, serving the same role as they did in previous games.

Visual changes

 * The graphics are greatly enhanced, patterned after the previous Nintendo 3DS Mario & Luigi installments.
 * The title screen is heavily altered, with the image being changed from a reflection of Peach's Castle and Bowser's Castle to Bowser inhaling everything in Peach's castle and the Bros. sitting in the Trash Pit on the bottom screen.
 * Mario's and Luigi's insignias on their caps are now red and green respectively, rather than black.
 * The Toads in Toad Town are now regular Toads with differently colored vests and spots, rather than differing in height and clothing.
 * Many locations have different color schemes.
 * Save Blocks have a new design.
 * The designs of the trees in Dimble Wood, Cavi Cape, and Plack Beach have been changed dramatically.
 * In the prologue scene at Toad Town, when the blorbed Toad crashes through the wall, it is shown in 3D.
 * The sparks that Mario and Luigi hit in the Arm Center minigame are modeled after the Sun for Mario and Saturn for Luigi.
 * After Bowser inhales everyone in the Conference Hall, he also inhales two statues of Peach nearby, one of which later appears in the Trash Pit.
 * When Mario and Luigi explore the Trash Pit after being inhaled, Bowser is facing away from rather than toward the player.
 * The floor sags slightly when the bros. walk around in some rooms inside Bowser's Body.
 * Enemy levels are now visible during battle.
 * The play time counter has been removed.
 * The camera briefly zooms in and then out if the player successfully gets an "Excellent!" on Bowser's punch.
 * Some quotes have been added or altered.
 * The ? Block that Broque Monsieur hits containing a healing item is now a Drumstick that heals Bowser instead of a Mushroom that heals himself.
 * Four of Bowser's command blocks have swapped colors: the Punch Block is red rather than yellow, the Flame Block is green rather than red, the Vacuum Block is yellow rather than green, and the Brawl Attack is blue rather than orange.
 * Bowser can now find coins in some trees using his Fire Breath.
 * After the player hits and saves on a Save Block (or loads up the game from the last save point), if the player's stats are low, a message will appear that reads: "Don't forget to restore your HP & BP!"
 * When hitting a Save Block, the player will be able to fully read the message the first time without needing to hit it again.
 * If the player uses Bowser's Fire Breath in the overworld on a Save Block, it no longer bounces briefly.
 * After finishing the Goomba Storm Brawl Attack for Bowser, he will raise his left hand to look up at the Goombas as they fall.
 * When the water fills in Pump Works, the Bros. will briefly float and sink back down.
 * After finishing the Fire Flower Bros. Attack, Mario will clean his hands, spin around and tip his hat, while Luigi spins around and does a finger gun motion.
 * The sprouts on the Leaf Guys' heads now flutter instead of spinning around like a propeller.
 * When Bowser gets crushed by a giant enemy, the background of his eyes will close.
 * The Green Orb in the Rump Command is a diamond shape rather than a round shape.
 * Bowser and Midbus no longer fight in a cage in Bowser's Castle before the boss fight begins.
 * The air vent that blows air out to turn Mario into Balloon Mario in the Pipe Yard to Peach's Castle is replaced by a platform.
 * Bean icons are now shown in the map after talking to the Toad in Toad Town that asks the player if they can tunnel underground.
 * Luigi now balances on the Super Bouncer ball when performing the Bros. Attack. He also bounces off of the enemy before kicking the ball down at them when the attack is performed successfully.
 * The little Blue Toad will remain next to the Badge Store in Toad Town after the player finishes hide and seek, rather than staying next to the blorbed Toad.
 * Bowser does not make a sneeze sound after he enters Blubble Lake.
 * Yikk now floats in the air instead of being on the floor.
 * The blue bubbles the Naplock blows out now has a Drumstick rather than a Mushroom.
 * Freeing a minion from Jailgoon will now give Bowser a Drumstick instead of a Mushroom.
 * Bowser Memory Neuron and Starlow will remain in the Memory Banks room instead of a blue background during a puzzle sequence.
 * In the boss battle against Bowser Memory ML, the Koopa Troopa Memory who would show up to bring Bowser Memory M back to normal size is absent, and Bowser Memory M shrinks by himself.
 * The Mushroom that enlarges Bowser Memory M is now a Mega Mushroom.
 * The Mushrooms and 1-Up Mushrooms Bowser Memory L uses are now memory-based.
 * Beef can be spotted in the Bob-omb Storage Depot which Bowser accidentally blows up. His presence there is explained in Bowser Jr.'s Journey.
 * The meteor in the Mighty Meteor Bros. Attack is now a 3D meteor that lacks the "?" icon. It also explodes into confetti unlike in the original.
 * In Broque Madame's Goomba Storm minigame, if enough Goombas have been burned, some will clump together into a ball before dropping onto Madame Broque's back.
 * Bowser now has a whistle during the Bob-omb Blitz Brawl Attack.
 * The roar sound when a Fawful Guy gets eaten and aimed at a bro for its attack is removed.
 * Big enemies in the overworld (apart from Toothies) no longer attack Mario and Luigi, although normal-sized enemies still attack them.
 * Puzzle Sacks now remain visible on the map after completing the Spin Pipe puzzle from Kuzzle.
 * The PR Toad that hosts Mushroom Ball Derby for the bros. to collect Mushroom Balls now opens all 16 of them rather than opening them one by one once they are found.
 * Bowser shoots fireballs out of his mouth at the Magikoopas during the Magikoopa Mob Brawl Attack.
 * The Bros. briefly show their breath when Bowser inhales Blizzard Midbus's frosty gas.
 * The Bros. can now jump off the sticky block in the Airway without Bowser's help to freeze.
 * The Dark Star now turns into Dark Bowser and briefly inhales Luigi after defeating it; in the original game, this happened before the fight.
 * Likewise, Starlow does not appear in both cutscenes when entering the pipe before hitting the ! Block and when the Dark Star transforms into Dark Bowser.
 * Bowser will now toss soap on Broggy when he uses Broggy Bonker Brawl Attack.
 * Kretin X now has a color scheme similar to its normal counterpart, albeit much darker.
 * The Dark Star X and the Dark Satellmites X have been recolored yellow with purple eyes, rather than being red with blue eyes as in the original version.
 * At the beginning of the Dark Star Core part of the final battle, Fawful briefly points at the bros before changing in size.
 * Peach's Castle now has a far darker appearance than before inside and outside and has far more Fawful logos upon Fawful's takeover and the Dark Star being unleashed with, when originally, it had minimal overall changes barring a more ruined appearance and Fawful's logo being strewn about.
 * Plack Beach is now partially flooded with water.
 * The Giga-carrot now has a bite mark to match the events of Bowser Jr.'s Journey.
 * Bowser is no longer shown when Durmite heals during the battle.
 * The trophies for beating Bowser Memory MLX and Dark Star X in the Gauntlet's trophy display screen have swapped places.
 * The 99 Block now starts at 99 instead of 0, decreasing with each hit.
 * There is now a statue for the Chakroad on top of Peach's Castle instead of being exposed.
 * The stage where Bros. and Brawl Attacks (along with regular attacks) are practiced is now a black and white version of Plack Beach rather than a starry stage.
 * In the final battle inside Bowser, Fawful now hangs on the ceiling if his legs are being attacked.
 * Likewise, Fawful now uses his arms and hands to crawl toward the Bros. while the Dark Star Core attacks.
 * When Bowser visits Broque Madame for the first time, she briefly alludes to Bowser Jr.
 * During the final battle, Dark Bowser's windstorm continues with debris flying over the top screen.

Audio changes

 * The title screen has new music rather than being an arrangement of the original game's title theme. The original music can still briefly be heard at the end of the credits.
 * Like in Mario & Luigi: Superstar Saga + Bowser's Minions, getting a Game Over plays a death jingle from Super Mario Bros., while in the original game, the music fades out.
 * There is a sound that plays whenever the player selects a Brawl Attack for Bowser.
 * Bowser's footstep sounds have been changed, and vary based on the current area he is in.
 * Fawful's voice sounds are slightly lowered in most instances, being pitched slightly higher near the very end of the game; however, his speech text sounds remain normal.
 * When Mario fights Bowser for the first time, the music that plays is the boss battle theme, rather than the regular battle theme.
 * After Bowser inhales everyone in Peach's Castle, the music does not stop until Midbus gives his line. In the original, the music stops after Bowser collapses.
 * The Cavi Cape music starts playing when the Bros. enter the Funny Bone instead of the Bowser Path music.
 * Fawful's main music plays when Bowser enters the room with food instead of his Castle music.
 * The Blubble Lake music starts playing when the Bros. enter the Toad Town pipe after defeating Bowser.
 * The tutorial music now plays while doing the puzzle in the Memory Banks.
 * After Luigi enlarges during the Snack Basket Bros. Attack, he will make a low-pitched laugh. When he lands on Mario after this happens, Mario will make an angry sound, and will grunt each time he pushes Luigi up.
 * The Dark Star and Dark Fawful now have their own battle themes; the Dark Star's theme is completely new, and Dark Fawful's theme is a slowed down cover of Cackletta's battle theme from Mario & Luigi: Superstar Saga. Despite this however, the Dark Star X still uses the normal boss theme.
 * Fawful's Plan music now plays during Super Peach's Castle of Fury's transformation instead of the Final Castle music.
 * This music also plays when the dark barriers in front of the castle are first created.
 * When the Dark Star Core changes into its true form inside Bowser during the final battle, Fawful does not laugh, rather laughing more quietly before he transforms. That laugh is instead used when he begins his chasing attack.
 * The music for the final battle now continues to play after the Dark Star Core is defeated.
 * Likewise, the battle music for the Dark Star and the Dark Star X also continues to play when they do their vacuum attack.
 * When Mario rescues Starlow and when both Mario and Luigi unlock the hammers, the jingle used when Bowser obtains the Vacuum Block is used instead of the regular item acquisition jingle.

Mushroom Kingdom

 * i Indicates they can be inhaled by Bowser and then fought by Mario & Luigi.
 * m Indicates only Mario can battle them.
 * m&l Indicates only Mario & Luigi can battle them.
 * b Indicates only Bowser can battle them.

Bosses

 * e Indicates the battle automatically ends after several turns.

Gauntlet Bosses
Note that all X bosses will only award coins after their first defeat. All these bosses are fought by Mario & Luigi.

Bowser Jr.'s Journey
This new addition to the main story sees Bowser Jr. as the titular character. While Bowser is occupied during the main story, this story sees Bowser Jr. on an adventure to cure the blorbs himself after it causes numerous minions to balloon up to an immobile state. The gameplay is very similar to Minion Quest: The Search for Bowser in the case that it involves two armies automatically fighting each other in waves, with occasional quick time events that can sway the battle in the player’s favor, such as captain commands which use CP, Button-mashing or button timing to defeat enemies, and special "Team-up" attacks that can be executed if the player has multiples of the same unit on the field. The rock-paper-scissors triangle of weaknesses returns, with Melee units being strong against Ranged units, ranged units being strong against Flying units, and Flying units being strong against Melee units. In this game, Bowser Jr. is always the captain and has the ability to change his unit type, though an additional First Officer slot is also available for Kamek or any of the Koopalings, with that unit having their own set of special abilities.

Story
The story begins in Bowser’s throne room in his castle. Bowser Jr. is seen rolling into the room on what appears to be a Goomba afflicted by the blorbs. Kamek explains the disease to Bowser, telling him there seems to be no cure as of yet. Their discussion is interrupted by Birdley, who appears to tell Bowser that a conference for blorb prevention is going on at Peach's Castle. Bowser, angry he was not invited, storms off to the castle with Kamek to crash the meeting. Unbenownst to Bowser, Fawful and Midbus are watching close by, ready to take over the castle (and also implied to have played a role in Bowser's not being invited to the meeting, specifically to lure him out of the castle). Fawful orders the Best Fitness Friends, Kaley, Dieter, and Beef, to infiltrate the castle while he goes to capture Bowser at Peach’s Castle.

Bowser Jr. assumes control in his father’s absence, and is seen fighting Captain Goomba and his Goomba squad multiple times. Nearby, Wendy and Roy discuss what to do about the blorbs, when the Best Fitness Friends appear to sell them their products. Although Roy shoos them away initially, they soon realize that their formula, Skeletone Formula:D, is able to cure the blorbs. Roy receives the recipe to make more Skeletone, which requires a Giga-carrot, an Omega Onion, and Ever Ice to create. Ludwig discusses a plan with the rest of the Koopalings to find the ingredients and cure the blorbs, while Bowser Jr, overhearing and thinking himself superior, sets off to find the cure himself. Ludwig decides to train Junior by teaching him the ropes of battle, using Captain Goomba, Boo, Shy Guy, and Koopa Troopa as examples. Roy joins Junior's team, followed by Ludwig and Morton. Larry challenges Junior, followed by Iggy and Wendy together, and finally the four minion captains again with King Bob-omb. Junior and the Koopalings (minus Lemmy, who stays behind to guard Bowser’s Castle), set off to Dimble Wood to obtain the Giga-Carrot. In the distance, Kaley, Dieter and Beef begin their plan to take over the castle.

As it turns out, it is revealed Fawful obtained the "Lucky Shroom" from Dieter to use on Bowser. Upon approach to Dimble Wood, Bowser Jr. witnesses Dimble Wood being inhaled by Bowser after eating the Vacuum Shroom. Kamek appears to brief the group on what happened before leaving, and leaves to look for Bowser once again, whom he lost sight of. After making their way through Dimble Wood, Ludwig begins to sense an uneasy feeling of being watched, and leaves the squad to find out. Soon after, they come across a few Shy Guys who were brainwashed by Fawful. Although Iggy points out the possibility of brainwashing, they dismiss the idea and trudge on. As they continue through the woods, Junior continues to irritate the Koopalings to no avail, berating Morton for not giving him his paintbrush and getting upset at them for not hurrying up. Roy, fed up, abandons the group. Kaley appears to warn the remaining Koopalings of the attack on the castle, so Wendy and Larry leave to go check things out, unaware that their plan was to lure all the Koopalings out of the castle and leave the base defenseless. Beef is able to dispatch Ludwig, and the Best Fitness Friends plan the defeat of the others. Finally, Junior, Iggy, and Morton reach the Giga-Carrot, but, since it is too big to pull out, Junior takes a small bite of it instead to take back. Kamek then finds Junior once more and joins him. Junior, Morton, Iggy, and Kamek head to Cavi Cape to search for the Omega Onion. They pass by the large hole at the exact moment Bowser uses the Chakroad, causing the two groups to miss each other. After Junior rudely tells Iggy to leave, he does so, only to get pushed off a cliff by Kaley, Dieter, and Beef, revealing their secret name as the Brute Force Federation. They decide to go for Roy next; meanwhile Junior takes Iggy’s lone clown car to use in battle. The group finds an Oho Jee carrying the Omega Onion, so they battle him for it. Afterwards, Kamek tells Junior the location of the Ever Ice, which was actually stored in the cryogenic chamber of Bowser’s Castle. Kamek had acquired it under Bowser’s orders to please Junior, but after he did not want it anymore, Kamek had stored the ice in the chamber in hope Junior might have wanted it again. Junior, Morton, and Kamek head back to Bowser’s Castle, with Kaley, Dieter, and Beef close behind, revealing that they plan to steal all the ingredients Junior collected to unleash the secret power of Skeletone Formula:D.

Meanwhile, Bowser’s castle is sent airborne by Midbus and is en route to Dimble Wood to attack Bowser. Dieter easily dispatches Lemmy, with Larry and Wendy watching from behind a wall. They help Lemmy, and although they try to escape, they are distracted by the castle landing (on top of Bowser), followed by Dieter trapping them in barrels. However, the rumbling of the castle due to Giant Bowser causes Larry and Lemmy to escape.

Upon approach to the castle, Junior realizes it is gone, and are confronted by several Goombas welcoming them to "Fawful Theater". After fighting the Goombas, several more come blabbing about Fawful Theater, and Junior gets bored with them, so despite the castle's absence, he heads down into the basement with Morton and Kamek. Upon reaching the cryogenic chamber, they retrieve the Ever Ice after a dangerous encounter with the Shroobs. Though all the ingredients have been collected, they still need to put all the ingredients together to make Skeletone, so Kamek suggests visiting Broque Madame at Blubble Lake for help. Before departing, however, Kamek makes Junior swear to aid the minions under the control of Fawful, regardless of whether it gives him personal glory or not. When they visit Broque Madame, Junior and the minions work together to give her a massage, and afterwards, she creates two hundred servings of Skeletone Formula:D. On their way back to Bowser’s Castle, however, Kaley and Dieter appear, steal the Skeletone, and mix it with another substance called Malodorius Fibbian to create the dangerous Malatone Formula:X. They use this formula to brainwash Morton, who easily dispatches Junior by tossing him into the lake. The evil trio reveals their plan to eventually betray Fawful as well once the entire army has been infected with Malatone.

Junior is found by Kamek washed up on Plack Beach. Although he maintains his bratty attitude at the start, Kamek tells Junior that his behavior has isolated everyone around him, and asks him to treat all the minions with more respect. As Junior takes out the charred drumstick that Morton gave him earlier, he remembers all of the times he berated the Koopalings, and begins to cry. This marks a turning point in Junior’s behavior for the rest of the game; he soon begins to enjoy the minions' company and speaks more politely to whoever he talks to.

Junior rescues Kamek after he is attacked by an army of Drillbit Crabs, and the two continue through Plack Beach to find anyone. They are soon attacked by several Goombas who were under the effects of Malatone Formula:X; meanwhile Kaley and Dieter were distributing lots of Malatone to lots of minions. Junior then decides to keep the promise he made to Kamek about saving the minions, and has Kamek come with him to be his witness. The two eventually find Iggy, who had acquired amnesia from his fall off the cliff. The star sage Kuzzle appears, claiming Iggy as his grandson “Charlie,” so they fight him to help him regain his memory. Iggy rejoins the squad, and the three pursue Kaley and Beef, who are on their way to Dimble Wood in a hurry looking for Ludwig, who seemed to have escaped the castle. Heading into Dimble Wood, they reach Kaley and Beef and prepare to fight. However, Ludwig had been disguised as Beef the entire time, and had actually defeated him a while ago and locked him in a Bob-omb storage room in Bowser’s Castle (this can be seen in the main game). Ludwig reveals all of the Best Fitness Friend’s goals, and defeat Kaley to end the chase. Ludwig presents Junior with RenewaLeaf, a substance that can remove the brainwashing of Malatone Formula:X, and informs Junior that the other Koopalings are at Blubble Lake.

At Blubble Lake, the Koopa Paratroopa Trio tell Junior that Larry and Lemmy ran in the direction of the castle, so Junior and his group head there. Along the way, they run into Mario, Luigi, and Starlow, with Starlow reassuring Junior that Bowser is working very hard. They find Larry and Lemmy, who are trying to help Bowser after he was crushed by the Tower of Yikk. As Bowser grows giant, Larry and Lemmy try to run in to help him, but get injured in the process, forcing Junior to rescue them before they get crushed, despite several brainwashed minions getting in the way. Junior apologizes to Larry and Lemmy for his behavior, and the group, now with four Koopalings, head to Bowser’s Castle to find Wendy, Roy, and Morton.

Upon approach to Bowser’s Castle, they find it has returned to its original spot. Kaley, Dieter, and Beef (who escaped from the Bob-omb storage room) arrive on the scene with Wendy in a barrel, and easily dispatch Junior and the Koopalings. Before they can finish things, however, Captain Goomba, Captain Boo, Captain Shy Guy and Captain Koopa Troopa all appear to help fight them back. Junior and his squad manage to deter the Best Fitness Friends and rescue Wendy, then give chase towards the castle. At the castle, they find Roy, who, ever since he left the group, was mercilessly attacked by numerous waves of brainwashed minions. On the verge of collapse after finally reaching the castle, Kamek heals him, but he is still too upset to listen to Junior. Junior challenges Roy to a 1-on-1 duel and wins, exhausting all his energy in the process. Roy, touched by this, rejoins the group, and they finally make their way to the final area.

In the castle, they find and cure Morton, thereby completing the Koopaling team. Now with all the Koopalings with him, Junior gives them his apologies for his past behavior and admits he only wanted to show-off before for Bowser. He also promises to be much better with them in the future. Junior, now filled with a stronger sense of leadership, leads the Koopa Troop to the final area, where the Best Fitness Friends await. As the world goes dark from the power of Dark Bowser, the Koopalings reminise on Bowser ordering them to look after Junior, and discuss if they managed to do that well enough. Junior and the Koopalings then encounter Kaley, Dieter, and Beef in the throne room. The trio sends out numerous waves of enemies, and eventually all three of them attack at once. When that fails, the three morph into a giant monstrous Malatone-infused creature with incredible power. Nevertheless, Junior and his troop defeat them for good, reclaim the Skeletone, and take back the castle’s control.

Junior and the Koopalings walk out to the castle balcony just in time to witness the Dark Star exploding outside. As Junior decides to wait for Bowser to return, they are interrupted by Roy, who had been distributing the cure to all the Goombas. The game ends with Junior following after Roy, to enjoy a party with all the minions. In the post credits scene, Junior attempts to console his dad after his loss to Mario and Luigi. He gives his father the Skeletone, which inadvertedly turns him into Dry Bowser after he eats the entire thing.

The player can go on extra challenges after the game is done, such as a fight with Bowser to prove to his father that he got stronger. Bowser can be recruited as a partner, and the remaining challenges include various fights with Malatone-infused minions in Plack Beach and finally a battle with dark Koopalings and Bowser in Bowser's Castle.

Nintendo eShop description
''Laugh your way through a hilarious story told from three perspectives! Search the Mushroom Kingdom for a cure as Bowser, explore his innards as the Mario Bros., and discover the untold story of Bowser Jr's Journey. Overcome the fury of Fawful, action-packed battles, puzzling tasks, and giant bosses in a classic action RPG-stuffed with new content! Mario and Luigi are stuck inside Bowser, forced to accomplish unusual tasks to assist their arch nemesis with hero stuff across the land. The scenes and dialogue that ensue will have you cackling like Fawful, even in battle! Time your button presses and keep up with the action: turn the system sideways, blow into the mic, or tap the touch screen. In an all-new mode, Bowser Jr. will cross paths with our unlikely allies as he recruits Ranged, Flying, and Melee troopers to fight for his cause. Strategically form teams and pit them against enemies to reign supreme in frenetic combat.''

Sales
Mario & Luigi: Bowser's Inside Story + Bowser Jr.'s Journey has had a poor launch sales record, being one of the worst-selling Mario games to date since the Virtual Boy, having comparable sales figures to download-only titles and Mario's Tennis, a stark contrast to the original release it was based on which remains to be the best-selling Mario & Luigi title. In Japan, it sold under 9,500 units in the first week and dropped off the top 20 charts by the second week. In comparison of the time period released and another remake of an older game, New Super Mario Bros. U Deluxe has sold 381,469 units in a lesser period of time. Comparing to other Nintendo 3DS ports of the Mario series released at a similar time frame on their first week, Luigi's Mansion and Captain Toad: Treasure Tracker sold 27,000 and 20,547 units respectively. . Famitsu's sales tracker reported the game as selling a total of 20,678 copies before falling off the charts, making it one of the worst-selling game in the entire Mario franchise.

Though not directly cited, the game's developer AlphaDream would begin bankruptcy proceedings on October 1, 2019, citing "sluggish revenues" as one of the factors. One gaming journalist also claimed that he was told by an inside source that Nintendo had "axed other 3DS plans" due to the game's poor sales.

Pre-release and unused content
During the Nintendo Direct on March 8, 2018, badges were shown to be available much earlier than in the original. In the final release, badges are obtained at the same point as in the original. It is unknown if this change was actually intended for the final product.

There are unused sprites in the game's files of Ludwig in a Clown Car like Iggy's, and unused sprites of Iggy on the ground in battle.

Among the unused sprites also include Bloopers, Golden Eggs, Toads with colors other than red, and differently colored Magikoopas on broomsticks.

Version 1.1
Date Released: 5 February, 2019

Nintendo eShop Update Content Description:
 * Depending on the event, sometimes the player got stuck on a certain map when controlling Luigi solo and trying to save the game progress by using the Save Block. The issue has been fixed.
 * By downloading the update data, this issue will no longer occur.
 * Also, if the issue has already occurred, it will be fixed so that the player can continue playing.

Version 1.2
Date Released: 19 March, 2019

Nintendo eShop Update Content Description:
 * Addressed an issue where sound wouldn’t play for music from the Nintendo DS version of Mario & Luigi: Bowser’s Inside Story in the Music Menu, under Records.