Pinky and The Brain are two genentically-altered lab mice whom due to a gene-splicing incident, gained the ability of speech and thought. While Brain uses his incredible intellect to plot for world domination, Pinky enjoys the simple things of life like cheese, lint and fez hats. The two mice are the "antagonists" of Animaniacs and the spin-off series, Pinky and The Brain. The two are secondary players in the Non Disney Villains Tournament.
Non Disney Villains Tournament
Brain resolves to take over NIMH, only to be thwarted at every turn by Martin Brisby. Irritated by Martin's insanity, Brain decides to take matters into his own hands. He thus shoots and kills his opponent with a laser.
Friends and Enemies
Brain joins forces with Mojo Jojo, another animal experimented upon by Mok Swagger. The two, along with their other allies, scheme to topple Mok's dictatorial reign over the animals, with Brain serving as the chief inventor of the faction. After the murderous Scarface attempts to kill the Brain's ally, General Woundwort, the Brain deduces his foe's loyalties: Napoleon must have ordered the assassination. Brain teams up with Drake and another associate, Jenner, to take down some of Napoleon's allies: Cat R. Waul and Warren T. Rat. During the battle, Pinky fires some fireworks off at Warren T. Rat and his cats. Brain further frightens away Warren T. Rat and crew, leading Warren T. Rat to be murdered by Jenner. Cat R. Waul is also defeated, scoring the Brain and his allies a victory.
In the wake of their victory, Jenner and the Brain have a meeting with Dolf, Napoleon's new financial backer. There, Jenner convinces the Brain to turn traitor against Mojo Jojo and help Napoleon. While the Brain still believes in the cause of the animal revolution, he consents out of dislike for Mojo Jojo.
The Battle of Animal Farm
The Brain's hour of reckoning occurs during the Battle of Animal Farm, in which Mojo Jojo's forces attack Napoleon's. Though Jenner dies early in the battle, the Brain still decides to turn against Mojo Jojo. When the monkey transforms into a giant, the Brain uses his own size ray in order to even the odds. He punches Mojo Jojo right into a building, causing to topple on top of the monkey. The Brain thinks he has succeeded, but Mojo Jojo gets up. Furious, the monkey blows smoke right into the Brain's face. The Brain heads to the top of a large building, waiting for Mojo Jojo to climb up to him. While Mojo Jojo hurls his fury at the Brain, Carface and a surviving Cat R. Waul set off one of the Brain's lasers, knocking Mojo Jojo off the building to his death. The Brain returns to normal size, only to discover that Dolf has killed Napoleon and taken over Animal Farm. Thinking for his and Pinky's safety, the Brain allies with the treacherous crow.
Death of an Innocent
When Dolf comes to Pinky and the Brain with a request to join him in a secret location, the Brain desires to come along. Pinky, terrified of Dolf and his desires, implores Brain to stay put. Brain, wanting to keep his standing, rebuffs Pinky and hurts his feelings, feeling terribly guilty because of it. Pinky thus stays, letting Brain go with Dolf. In the middle of the meeting, Zero announces that he desires to take over Animal Farm. When Dolf refuses to back down, Zero blows up one of Dolf's laboratories, the very laboratory that Pinky is in. Brain is too late to stop his friend from being blown to smithereens.
Swearing vengeance upon all of humanity after Pinky's death, Brain grows erratic. He employs the mutation rays of Dolf's newest ally, Blackwolf, to transform a helpless scientist into an insectoid monster. Brain is later summoned by Rupee, as the turkey warns the Animal Farm's members, about Dolf's uprising and the danger he possess. However, Rupee is silenced by Cat R. Waul, as the evil cat imprisons him in Dolf's jail.
In "War of the Villains", Both Pinky and The Brain were used as the power source to Mechanicles' latest invention to clean the deserts of Agrahbah. Fed up by his mistreatment, Brain freed himself and Pinky from their cage to plot vengance on Mechanicles. While Pinky wondered how Brain would do it, Brain explained he would overpower Mechanicles' mechinizim. He was successful in his attempt and he and Pinky escaped as the vessel soared away into the sky.