The gangster Babyface and his men break into a candy factory and break open the safe. Two heroes arrive to stop them: Elongated Man and Plastic Man. The villains have no idea who Elongated Man, much to the hero’s dismay. He complains about how Plastic Man is more popular then him, and Plastic Man admits that Batman prefers to hang out with him. They split up to take down the criminals. When Plastic Man spots some of the loot, his greed gets the better of him and he tries to take it, but Elongated Man stops him. Finally only Babyface is left and he tries to make a run for it. The two heroes fight over who will capture him and end up tangled together. They fall into a taffy puller and Babyface heads for the door... only for Batman to knock him unconscious. When the heroes ask which one he prefers, he tells them that as far as he’s concerned, he’d rather work alone.
Physicist Ryan Choi is working on a vital experiment in his laboratory when he gets a phone call from Aquaman. Aquaman explains that he and Batman were battling the gigantic chemical-spewing monstrosity known as Chemo, and Batman was hit by a blast of chemicals. Ryan Choi activates his size & weight controls and transforms into the Atom. Riding the phone lines at the size of an electron, Atom emerges at the other end and examines Batman. The Caped Crusader has been infected with a silicon virus that can replicate. Aquaman wants to know if Atom has a cure and he admits he’s not a doctor of medicine. Chemo is renewing his attack on a nuclear facility. With time running out, Atom says he’ll have to enter Batman’s body and battle the virus. Aquaman insists on going with him and Batman agrees. Before they depart, Atom warns Batman not to exert himself as it will cause the virus to spread faster.
Atom and Aquaman shrink and dive into Batman’s mouth and down into one of his lungs. Meanwhile, seeing that the Navy is having no success against Chemo, Batman takes the Batmobile out into the ocean and attacks the creature. He starts to weaken and is forced to submerge when Chemo attacks him. With his oxygen leaking away and his motor control deserting him, Batman switches to voice control and orders the Batmobile to the surface just in time.
Atom and Aquaman finally spot one of the virus/creatures in Batman’s lung. Aquaman cuts it in half with a water sword, but the pieces replicate into more virus/creatures. Atom insists they need to take a thinking man’s approach to the problem and after a few minutes of consideration, produces an electro-shock gun and blasts the viruses. He destroys them but a new wave attacks. Atom realizes that the virus/creatures are replicating themselves faster because Batman is exerting himself. With the virus/creatures closing in, Aquaman takes charge and hustles Atom into a blood vessel. The King of the Seven Seas telepathically summons a "sea creature": a lymphocyte that he uses as a mount to escape. Aquaman christens it "Platelet."
Batman renews his attack against Chemo but is unable to stop it getting to the nuclear facility.
Aquaman, Atom, and Platelet finally evade the pursuing virus/creatures and Atom realizes that they’re hopelessly outnumbered. The only way to defeat the virus/creatures is to take out the seed cell, which has taken root in Batman’s brain.
Chemo takes a nuclear missile from the facility and Batman realizes that someone is directing the creature’s actions. Chemo’s controller reveals himself: it’s the Brain, who tells the nearby city to surrender. The Brain orders Chemo to swallow the missile, then threatens to have Chemo dissolve it within him and detonates the warhead if the people don’t surrender. With conventional weaponry useless, Batman ejects from the Batmobile and leaps into Chemo’s mouth.
Aquaman and Atom find the seed cell at Batman’s brain. However, its virus/creatures mutate into a new form and become much stronger. Atom realizes that Batman has been exposed to Chemo’s chemical toxins again.
Chemo attacks the city while a weakening Batman in aquatic gear swims to the missile. He deactivates it and then blows open the side of Chemo’s chest, causing the chemicals to escape and leaving Chemo as a deflated husk. Batman spots the Brain’s submarine in the harbor, monitoring the attack.
With the virus/creatures closing in from all sides, Atom is fresh out of idea. Aquaman is tired of all the thinking and launches himself and Platelet into battle to distract the virus/creatures while Atom comes up with a plan.
Batman enters the Brain’s sub but collapses. However, fortunately he knocks over the Brain’s containment device, leaving it flat on its back.
The virus/creatures destroy Platelet, and Atom has finally had enough. He physically attacks the virus/creatures, blasting them back. An impressed Aquaman joins in and Atom gets to the seed cell and destroys it by smashing it with one of his weapons. All of the virus/creatures dissipate when the seed cell is eliminated.
Both Batman and the Brain try to right themselves. The Brain succeeds first and extends tentacles to cut Batman open. However, all traces of the virus disappear from Batman and easily defeats the villain, removing his brain chamber from its containment vessel.
Aquaman and Atom celebrate their triumphant, and Aquaman can’t help pointing out that it was brawn, not brain, that won the day. Atom admits it was a momentary lapse of judgment on his part. After pausing for a moment to honor Platelet, the heroes look for a way out. Atom takes toward Batman’s tear duct, while Aquaman notes that the Caped Crusader never uses it.