The Big Guy is decommissioned in favor of Quark Industries' newest creation, Rusty the Boy Robot. But when an alien Annihilator threatens to destroy New Tronic City, it's clear that Rusty is not quite ready for prime time. The Big Guy is reassembled and joins the fight along with Rusty. General Thorton orders that the temporary alliance become a permanent partnership.
The Big Guy and Rusty face off against the Legion Ex Machina's evil creation: A.R.G. -12, a.k.a. Argo. When a Nucleo-Protonic blast from Argo triggers a malfunction in Rusty's power core, the boy robot fears that he will be disassembled due to the fact that he is going out of control.
A telepathy experiment goes awry and a Quark Scientist, Dr. Neugog, is transformed into a giant brain on spidery legs. Neugog uses his telepathic powers to drain the minds of the world's greatest scientists. Meanwhile, Dr. Slate accidentally discovers that there's a man in the Big Guy suit.
Rusty tags along with Dwayne to his nephew's birthday party. Rusty's present is a piece of stolen alien technology, known as a Dimetrium Agglomerator. The aliens, Emek and Naard, own the Agglomerator and come to claim it.
Dr. Gilder, the Legion Ex Machina's mole within Quark, has developed a personal grudge against Donovan, so he takes control of a prototype and tries to assassinate him. Donovan is taken to the S.S. Dark Horse for his own safety. Gilder then hacks into Rusty, gives him a ""big gun"", and sets out to destroy Donovan.
Dr. Slate, Big Guy and Rusty find out that the Legion Ex Machina's mysterious ""final assembly"" is taking place in a network of underground tunnels. When Big Guy and Rusty find the tunnels, they derail a robotic train. Inside the massive train's cargo hold is a gigantic hand that boasts a built-in high-tech cannon. With their plan uncovered, the Legion Ex Machina members decide to activate their latest creation ahead of schedule and missing a hand.
The Legion Ex Machina downloads Rusty's programming in an effort to learn his secrets. Rusty, Big Guy and the Evil #4 end up in a showdown in cyberspace.
While trying to keep the Legion Ex Machina's newest robot from absconding with Quarks' new anti-neutrinos, Rusty plugs into the bot's software to learn the Legion's secrets. #4 counters Rusty's hack by engaging in a mental tug of war. A power surge switches personality traits between the two robots. Rusty starts building a doomsday machine while #4 plays video games.
Donovan unveils Quark's latest prototype: tiny liquid metal robots called Nurds that repair and upgrade any technology they come in contact with. When Big Guy becomes infested by the Nurds, they repair its original artificial intelligence circuitry, making Big Guy a fully functioning robot, which removes Dwayne from the pilot's seat. But shortly after the new Big Guy successfully completes his first mission, things go awry.
On Quark Industries' recently christened space station, the computer, known as Edie, has gone mad. Threatening to destroy the moon, Edie demands delivery of the Ubik Chip, which would allow Edie to gain control of all computers on Earth.
Big Guy and Rusty journey to the heart of a volcano that erupted in the city to deliver a Cobalt Thorium-G Bomb. They are suddenly attacked by magma creatures, who turn out to be the ones engineering the volcano in an attempt to take over the surface world.
Being powered up for six months, Rusty has not grown an inch. Frustrated that he will never be as big as The Big Guy, he connects his robot head on the powerful robot body of Quark's T-7000 Prototype. But he learns there's more to crime-fighting than just being big when a gang of exosuit-wearing chopshoppers (Gage, Big Rig, and Cargo) lure him into an ambush.
A family of aliens, made of organic metal, come to earth seeking refuge from their pursuers, evil insect-like robots.
When Quark's Dr. Kirby disappears after an experiment with his Quantum Machine goes awry, a hostile monster emerges and goes on a rampage, apparently having destroyed the doctor. Back at Quark, Rusty discovers a previous ""boy robot"" prototype. Hoping for a new friend, Rusty reassembles the robot, who he names ""Earl."" But Earl's relentlessly aggressive programming turns him against the heroes.
Quark develops a protoplasmic, semi-intelligent blob that doubles as a cleaning agent. The title is given as a ""Squeaky Gleem"".
Donovan's nephew, Pierre, is working on a robot for the school science fair. He uses the brain of the Legion Ex Machina's #4, who was recently captured by Quark. When it's activated, trouble ensues.
Big Guy and Rusty go back in time to the civil war.
A former military comrade of Duane's gets hired at Quark. He quit the military because he thought the pursuit of a robot without a human was wrong. Now he has created his own version of Big Guy, ""Hard Drive"", and with it plans to destroy what he thinks is a pure robot.
Quark releases an alkaline-powered, non-flying version of Rusty for consumers. However, the Legion Ex Machina manages to gain radio control of the Rusty knock-offs, and attempt to use them to destroy New Tronic City.
An intergalactic thrill-seeker named Po the Obliterator comes to challenge Earth's greatest champion, The Big Guy.
A virus-carrying alien threatens the world, and Dr. Slate must take the helm of Big Guy.
Pierre becomes a brain-sucking monster when he plays around with Dr. Neugog's telepathy helmet. Quark uses the fiendish Neugog to track him down.
Jellyfish create duplicates of the crew of the new Quark research centre at the ocean floor.
The Legion Ex Machina creates a Big Guy duplicate.
Big Guy and Rusty find the Legion's headquarters and rescue the creator of the Big Guy armor, who Rusty refers to as Big Guy's dad.
Giant jungle animals wreak terror in the Congo.