Now on his own, Ben sets out to be a solo superhero, with new alien heroes at his disposal, but Grandpa Max has other plans. (Introducing Rook, Malware, Khyber, Nemetrix alien Crabdozer, new Ben aliens Feedback and Blox, Pakmar)

Ben and Rook discover an underground city beneath Bellwood populated with aliens! But who is terrorizing them? (Introducing Nemetrix alien BugLizard, and Ben alien Shocksquatch, Psyphon, Fistina, Bubblehelmet, Liam)

Alien pests from Ben's youth come back, but now they need Ben's help. (Introducing Fistrick, and new Ben alien Gravattack)

Flashback episode: Young Ben, Gwen, and Grandpa Max visit Azmuth on Galvan Prime. There, they have their first encounter with Malware, a corrupted Mechamorph who's determined to make Azmuth cure him, by any means!

Ben and Rook must stop a giant rampaging alien from destroying Bellwood while dealing with a peace-loving alien-rights activist who doesn't want it hurt. (Introducing Hokestar, Solid Plugg 1st appearance, Pax, Sunder)

Dr. Animo has escaped his Plumber prison, and Ben and Rook must track him down before he turns the world into his personal mutant ant farm!

When Ben and Rook investigate a mysterious alien ghost ship, they discover that Argit and the Vreedle Brothers are fighting for possession of a doomsday device!

Ben and Rook encounter a race of elastic, hot-blooded aliens in Undertown who want to use a stolen nuclear fusion engine to activate a volcano!

Khyber and his Omintrix possessed pet have been testing Ben's skills and gathering information. They now use their collected knowledge to finally face Ben in battle.

While trapped in Khyber's ship, Ben learns details about the origin of the Nemetrix, and the link between Khyber, Malware, and Dr. Psychobos!