The Brain set its base in northern India where it used special collars on the local wildlife to mind-controll them. The animals attack everyone who comes close to the base. He also uses his right-hand man, Gorilla Monsieur Mallah, to dispose of intruders.
When the Young Justice team, accompanied by Captain Marvel, arrive at India to investigate, the animals capture Captain Marvel and bring him to his base. There, he plans to extract Marvel's brain in order to learn his secrets and knowledge.
When he is alerted that the rest of the team is coming for Captain Marvel, he sends Mallah out to capture them as well. He continues to prepare for the brain extraction but is attacked by the tiger Shazam befriended earlier. The team then breaks through the wall into the operation chamber and Robin recognizes The Brain.
While the team fights Mallah, the Brain decides that the battle is lost. To escape, he deactivates the light inside the base and he and Mallah escape in the cover of darkness.
At the end of the episode, the Brain is revealed to be one of the leaders of the secret organization known as The Light.