General Warhawk and Sergeant Havoc capture a young monk who would become the next Dalai Lama and gains control of a small village in Tibet.
Killbane breaks into Longshot and steals one of the components of Mindnet, a device that induces psi abilities, for the Queen of the Crown.
The destruction of Quintessa causes the Autobots to arrive at Goo and poor Springer loses some parts. Blurr and Wheelie are stuck in a hostile place and are in need of some help. Meanwhile, the Quintessons agree to give vital energy to the Decepticons so long as the Autobots are destroyed.
The Joes send teams out to guard the tombs on Zartan's list, but each team is defeated in turn: by Zarana in Egypt, the Crimson Twins in Paris, the Dreadnoks in the Yucatan, and the Baroness in Transylvania. Duke's team and the Oktober Guard are in a standoff with BATs while defending the tomb of Ivan the Terrible.
The Joes are reunited with old friends (The Oktober Guard), and face new enemies (The B.A.T.'s and new Dreadnok's) as COBRA commences it's DNA extraction operation for the creation of Serpentor.
A surprise attack by Cobra, using the new BATs, reveals that the Joes have gotten sloppy. General Hawk asks Sergeant Slaughter to help whip the team back into shape. Meanwhile, a series of dreams prompt Dr. Mindbender to concoct a plan to build a new Cobra leader from the DNA of long-dead conquerors. A package downed Night Raven reveals that Zartan has been asked to expand his team of Dreadnoks so he turns to his siblings, Zandar and Zarana for help, and the Joes investigate and discover the plan, only to be cornered by Thrasher and his Thunder Machine.
Dissatisfied with Cobra Commander's leadership, Dr. Mind Bender proposes genetically creating an ideal new leader.
The Autobots make it out of Charr, but Rodimus is down and looks out. In reality, he has made a trip to the Matrix and learns the Quintessons are behind the kidnapping. After Rodimus is revived, a rescue mission is soon underway. Also, Scourge and Cyclonus finally track down a battle hungry Galvatron.
The continuing adventures of the "now adult" Beaver Cleaver, his family, and their friends.
The Limbo bank is robbed by a bandit with an uncanny resemblance to Quicksilver.
General Warhawk is in Chicago to rob a money shipment to the federal reserve bank. Rambo, suspicious that the backup troops are late, learns that those troops have been replaced by Warhawk's men...
The Rangers search for Eliza's psychocrystal. Geezi is a snitch, and he has one of the Queen's memory birds. The Rangers go back to Tortuna to buy the bird from Geezi, and they learn about how the Queen has decimated the Gherkin race along the way.
While everyone continues to rejoice in their victory, unknown assailants capture Ultra Magnus, Kup and Spike. After being told by a alien, a group of Autobots suspect the Decepticons are the culprits. But when they arrive at Charr, they find the Decepticons in no shape to pull off a kidnapping, meaning another is responsible.
A genetically engineered reptile man, built by the army as the ""ultimate weapon,"" goes out of control and Dr. Quest and the team are called in to stop it.
Del, Rodney, and Albert are mistakenly apprehended as shoplifters by an overzealous security guard at the Top Buy Supermarket. And things get worse when they're taken to the manager's office and realise that they've lost their receipt for the goods. Shortly after, Tom the security guard brings a cocky shoplifter, Lennox Gilbey, into the manager's office, where he promptly pulls out a gun and demands money from the safe. Unluckily for Lennox the safe is on a time-lock and due to the dodgy watch he's wearing, he's 15 minutes later than he planned - and the safe doesn't ...
Zachary Foxx is assigned on a mission to observe a small group of humans who have established a home on the planet Kirwin. Captain Foxx travels with his wife, Eliza, their two children and Alien diplomats Zozo and Waldo.
Chummi Gummi comes to Gummi Glen in search of the Great Gummis. When he finds there not there he goes to search for them. Cubbi wants to leave with him so he can become a knight.
The twins decide to get some snacks from the kitchen but Piggy warns them of the consinquences for getting snacks without Nannny's permision they ignore her warning but when piggy tries to sneak the snacks back in the kitchen Nanny accuses her of stealing from the fridge and makes her clean up the mess.