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One day, in his room, Hiro accidentally activates Baymax and discovers a single microbot left in his jacket. Baymax believes the microbot is trying to go somewhere and he and Hiro follow it to an abandoned warehouse, where they discover that someone has been mass-producing Hiro's microbots, and are attacked by a masked man controlling them.
Realizing the masked man has stolen his project, Hiro decides to catch him and upgrades Baymax with armor and a battle chip containing various karate moves. After the masked man attacks Hiro, Baymax, Gogo, Wasabi, Honey and Fred, the group decides to join Hiro in the fight, and Hiro makes each of them a suit of their own. After the attack, the group met at Fred's house where he with all his knowledge of comic books convinced them that the guy with the mask is a tycoon named Alistair Krei that is mad at Hiro because he offered to buy the microbot technology at the school exhibition but he refused. So they decided to search Krei and demand justice.
With the help of his upgraded eye scanner, Baymax locates the masked man on a quarantined island. There, the group discovers a former lab of Krei Tech where they tested a teleporter that exploded when a human test pilot vanished inside the unstable portal. After a brief fight, the masked man is revealed to be Professor Callaghan, who explains he started the fire so he could steal Hiro's microbots. Realizing that Tadashi died in vain, Hiro angrily removes Baymax's healthcare chip, leaving him with only the battle chip, and orders him to kill Callaghan. Baymax almost does so until Honey manages to insert his healthcare chip back in.
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Angry at the group for preventing his revenge, Hiro goes home but breaks down when Baymax asks him if killing Callaghan will make him feel better. To soften Hiro's loss, Baymax plays many clips of Tadashi running tests on him during Baymax's development. Hiro realizes that killing Callaghan is not what Tadashi would have wanted and makes amends with his friends.
The group discovers that the test pilot was Callaghan's daughter Abigail and realize that Callaghan is seeking revenge on Alistair Krei, whom he blames for her death. In the HQ of Krei Tech, Callaghan opens a portal that will absorb all the Krei complex and Alistair with it. Hiro and his friends arrive to the place and after a brief fight they save Krei and destroy the microbots, but the portal remains active, becoming increasingly unstable. Baymax detects Abigail from inside the portal and he and Hiro rush in to save her. On their way out, Baymax's armor is damaged and he realizes the only way to save Hiro and Abigail is to stay behind to propel them forward with his rocket fist. Hiro refuses to leave Baymax, but Baymax insists until Hiro tearfully gives in. Hiro and Abigail make it back, and Callaghan is arrested.
Baymax scan the portal and detects Abigail from inside the portal and he and Hiro rush in to save her. On their way out, Baymax's armor is damaged and he realizes the only way to save Hiro and Abigail is to stay behind to propel them forward with his rocket fist. Hiro refuses to leave Baymax, but Baymax insists until Hiro tearfully gives in. Hiro and Abigail make it back, and Callaghan is arrested and everything comes back to normal, excepting that Hiro is alone again. Sometime later, as Hiro seems to feel better, he discovers Baymax's healthcare chip, which contains his entire personality, in his rocket fist. Delighted, Hiro rebuilds Baymax and they happily reunite. The six friends continue their exploits through the city, staying unknown, and fulfilling Tadashi's dream of helping those in need.