The Koopa Bros. are a quartet of costumed ninja Koopa Troopas consisting of Green Ninjakoopa, Yellow Ninjakoopa, Black Ninjakoopa and the leader, Red Ninjakoopa. A spoof of the Teenage Mutant Ninja Turtles, the team appeared in Paper Mario as the bosses of the first chapter. They live in Koopa Bros. Fortress and are part of Bowser's Koopa Troop.
While the Koopa Bros. are all egotistical and obsessed with being cool, they have a great deal of respect for both Bowser and each other. They were entrusted by the Koopa King to guard Eldstar, and Mario defeated them first in Paper Mario. The theme that played during the fight with the Koopa Bros. is a remix of the Hammer Bros. theme from Super Mario Bros. 3.
It is mentioned by several characters throughout Paper Mario that the Koopa Bros. were originally inhabitants of Koopa Village, apparently living in it around the same time as Kent C. Koopa. It is hinted by Russ T. that Kent C. Koopa trained the Koopa Bros. in combat. Eventually, the Koopa Bros. grew tired of Koopa Village, finding its serene environment and lack of excitement boring. They eventually left and traveled to a fortress that would become their own, whose Bob-ombs they took command of.
According to the Bob-ombs that were jailed in the fortress, the Koopa Bros. became conceited and corrupted due to the influence of Bowser and Kammy Koopa, who had taken a liking to them. The resident Bob-ombs were enslaved and worked non-stop. Those that rebelled were jailed, and the indigo Bob-ombs that Mario ends up fighting within the fortress were all supplied by Bowser to take their place. When Bowser stole the wish-granting Star Rod and imprisoned the Star Spirits, the Koopa King entrusted the elder Star Spirit, Eldstar, to the Koopa Bros.
The Koopa Bros. first appear in Paper Mario in Peach's Castle after the Goomba King's defeat, where they reassure both Kammy Koopa and Bowser that they can stop Mario, and also show them a special technique, which impresses Bowser. Soon after revealing their attack, the Koopa Bros. are sent from Princess Peach's Castle back to their fortress after informing Bowser that they did not actually post someone to guard the captured Eldstar, a show of incompetence and lack of thought which infuriates Bowser.
At first, the Koopa Bros. simply attempt to stop Mario from reaching Pleasant Path and their fortress by disguising themselves as dark colored Toads under the name Nash T. (a pun on "nasty") and blocking the path to those locations, saying that dangers lurked there. With help from Merlon, who sees through the Koopa Bros.' disguise and removes it with his magic, Mario is able to make them retreat.
When Black Ninjakoopa finds that Mario and his allies have reached Koopa Bros. Fortress, he alerts his brothers and they proceed to set about making various traps and obstacles in their home, all of which Mario passes. Yellow Ninjakoopa in particular lays a trap involving a ? Block which activates a trap door below it when struck, which places Mario in the same jail that the rebel Bob-ombs reside. In a last-ditch effort to stop Mario, Red Ninjakoopa has his brothers set up three Bill Blasters on top of the fortress, which Mario also manages to overcome. Reaching the Koopa Bros. at last, Mario, before he can fight the Bros. themselves, has to battle their creation, a poorly constructed facsimile of Bowser. When their fake Bowser is destroyed, the Koopa Bros. attack Mario using a whirling tower attack. The Koopa Bros. battle optimizes the abilities of Bombette and Kooper; Bombette's Bomb attack can knock over the Koopa Bros. stack instantly, while Kooper's Power Shell can hit all of them at once. Mario is able to defeat the Koopa Bros., sending them into the prison. It is revealed that the rebel Bob-ombs, before escaping, patched the hole through which they escaped with two planks of wood and nailed them in place. This temporarily prevents the Koopa Bros. from escaping.
After the Koopa Bros. are defeated, they send a letter to Mario's House. In the letter, the Koopa Bros. swear revenge on Mario, with each leaving a unique threat. Also, for a short while after their defeat, the Koopa Bros. are found in the prison of their fortress, bumbling around. However, if Mario visits it later, they are gone, indicating that they eventually managed to escape, though the wooden barricade remains. There is also a piece of Toad Town News documenting their defeat.
In Chapters 4-6, the Koopa Bros. under the Nash T. name are said to "rule the street" according to the scribble on the back side of the Toad Town notice board.
In Chapter 8, the Koopa Bros. appear at Bowser's Castle under the employ of the castle's third Guard Door. The Koopa Bros., who claim to have become stronger (even renaming themselves "the Super Ultra Mighty Koopa Bros. the Great"), prepare to fight Mario, but are all easily knocked away by a determined Jr. Troopa. When Mario beats Jr. Troopa, the Guard Door reasons that since Jr. Troopa defeated the Koopa Bros. and Mario defeated Jr. Troopa, Mario has technically completed the task assigned to him and lets him pass.
During the ending parade of Paper Mario, the Koopa Bros. appear riding a float built from the remains of Bowser???. As the Koopa Bros. strike a pose, several Bob-ombs appear and explode near them, covering them in soot.
In addition, a Koopa Brother can be seen watching the Chuck Quizmo show.
In volume 1 of Super Mario-Kun, a Japan-exclusive manga, nine years prior to the release of Paper Mario, a similar group called the "Mutant Ninja Sentai Nokonoko (Koopa Troopa) Men" appear to attack Mario, Luigi, and Yoshi in a platform-filled area, taking on various disguises and using shell-like shurikens in combat. The Koopa Bros.' true appearance in the manga is volume 25, where, like their game counterparts, are first encountered by Mario, Goombario and Kooper disguised as Toads.
The leader of the Koopa Bros., Red Ninjakoopa has authority over his siblings and seems to come up with their plans. When Mario reaches the roof of the Koopa Bros. Fortress, Red Ninjakoopa has the other three Koopa Bros. open fire on him with a barrage of Bullet Bills.
Black Ninjakoopa is the possible second-in-command of the Koopa Bros. and the one seen apart from his brothers most often. When Mario reaches Koopa Bros. Fortress, it's Black Ninjakoopa who reports this to Red Ninjakoopa and his other brothers, who fortify security in response. Additionally, when Mario first enters the chamber where he battles the Koopa Bros., it's Black Ninjakoopa who appears to greet him, before leaving with Red Ninjakoopa to pilot the Bowser???.
When Mario gets deeper into the Koopa Bros. Fortress, Yellow Ninjakoopa sets a trap for him; when Mario hits a rigged ? Block, a trapdoor opens beneath him and sends him falling into the Koopa Bros.' dungeon; as Mario falls, Yellow Ninjakoopa taunts and jeers at him.
However, Yellow Ninjakoopa's plan of trapping Mario in the dungeon backfires, as Mario meets Bombette in the dungeon and also manages to break several other Bob-ombs out of it. He is apparently the third-in-command of the Koopa Bros.
Upon being alerted to Mario's arrival at the Koopa Bros. Fortress by Mario, Green Ninjakoopa takes defense precautions and has a key sealed away and guarded. When Mario finds Green Ninjakoopa while he is doing this, the Koopa Bro taunts Mario and flees. He also appears to be the last-in-command of the Koopa Bros.
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