Robin, Aqualad, and Kid Flash break into Cadmus and find that it is being run by Genomorphs.

The sidekicks find a clone of Superman known as Superboy. They free him from Cadmus' control, while battling Blockbuster.

After Speedy declines to join the new team, Robin, Aqualad and Kid Flash fear Young Justice is just a big joke…while new member Miss Martian fears there's no room for her to be part of it. So when the four heroes and Superboy come up against Mister Twister, it looks like all their fears have just been realized…

Young Justice goes on its first official mission under Batman, while trying to determine which of them will lead the team.

Superboy's anger over his non-relationship with Superman is getting out of control. He refuses to train with Black Canary, and when the team faces an opponent that even the Justice League had trouble defeating, the Boy of Steel goes rogue.

Green Arrow's niece, Artemis, joins Young Justice and must save a bright young scientist from the League of Shadows.

When the team investigates the disappearance of Kent Nelson (formerly Doctor Fate), the scientific-minded Wally West is forced to confront his disbelief in magic while battling Abra Kadabra and Klarion the Witch Boy, for the ultra-powerful Helmet of Fate.

After a disastrous mission with the team, Aqualad returns to Atlantis to choose between a life on the surface world or one beneath the waves with the Aquagirl of his dreams. But other forces at play may make Aqualad's decision for him.

Young Justice discovers that they have forgotten the last six months of their lives, including each other and a final fateful mission in Bialya. The team turns to Miss Martian to recover their memories, before it is too late for Superboy.