It's a rainy night in the jungle, and Mento informs the Teen Titans of how the Doom Patrol have fought the Brother of Evil – the immortal soldier General Immortus; the stretchable Madame Rouge; the supersmart gorilla Monsieur Mallah; and their leader, the Brain. Now that they have built and powered the Quantum Accelerator, they will use it to control the world.
They manage to locate the Brain's mountain base based on Mento's reading the villain's mind. Mento invites Beast Boy along and the Titans insist on going with them. Beast Boy tells them not to then departs with the Doom Patrol. Robin decides they'll go along with them anyway.
The Doom Patrol makes their way through the jungle and Robotman starts to go down into quicksand. Negative Man and Elasti-Girl pull him out and Beast Boy starts to have second thoughts that they can't handle the situation. Beast Boy spots a robot behind them and it attacks – it's proof against all their powers as it freezes Elasti-Girl and enmeshes Negative Man in an energy cave, while using a magnetic force field to repel Robotman. Beast Boy takes out the robot and they leave as the robot revives long enough to open fire on Beast Boy. Robotman manages to take it out by sacrificing himself and the others head on, but the Brain is aware they're coming.
As the Doom Patrol prepares to cross the desert, they see Robotman destroyed in the distance and Mento orders them to continue even though Beast Boy is reluctant. Halfway across General Immortus orders an attack and robot tanks close in on the Patrol. They take out the tanks and Immortus fires missiles at them. They spot an opening and head for it, realizing it's a trap but having no choice. It's a magnetic minefield and it activates as dozens of robots and tanks surround them. Negative Man draws the mines off as the others run, then redirects the mines back at the tanks. But his negative self is unable to reach his body in time and fades into the earth. Elasti-Girl catches a falling rock so Mento and Beast Boy can escape – Mento refuses to let Beast Boy go back. Beast Boy scouts ahead then calls in the Titans, but Mento spots him and destroys his communicator, refusing to let the Titans die along with them. Beast Boy realizes it's a suicide mission.
Beast Boy refuses to go with Mento and takes off the mask Mento gave him. Beast Boy suggests they follow Robin's advice and comes up with a new strategy. After nightfall, Mento scans the building and Beast Boy and Mento disable the weapon systems and stroll in. Beast Boy smells something and the two head down a side tunnel, unaware the Brotherhood know where they are. The building is psychically shielded against Mento and Mallah and Rouge attack. Beast Boy takes out Mallah and Mento probes Rouge for Brain's location, without success. He slows her down long enough to mentally knock her out and then they make their way to the Quantum Accelerator, where more robots commanded by General Immortus surround them. They open fire and Mento protects them long enough for Beast Boy to get to the Accelerator. The Titans make their entrance along with other Patrol members and they take out the robots. Beast Boy starts to reprogram the accelerator but is captured by Brain, Rouge, and Mallah. The Brain orders a demonstration on Titan Tower and the city around it, and Mento and Robin order an attack. More robots emerge and Mallah and Rouge enter the battle as well. Beast Boy gets free and redirects the Accelerator to the base they're in, knocking the Brain off the pedestal. The villains grab the Brain's…brain and run, while the heroes take out the robots then get out of the base as the black hole forms and destroys the complex.
Afterward the two teams part on good terms and Mento vows they'll be waiting…and will call on the Titans when they need them. Elsewhere, the Brain vows to destroy the Titans and all the young heroes in the world…and has assembled every Titan villain to carry out his plan.