Season 2 - Episode Guide

Black Canary convinces Green Arrow to help save her mentor, Wildcat, from his involvement in an underground, super-powered fight club known as MetaBrawl.

Mister Miracle and Big Barda solicit Justice League assistance to free Oberon from Apokolips. J'onn refuses, but Flash decides to help out on his own.

Superman battles Doomsday in the heart of a volcano. Doomsday is revealed to be a modified clone of Superman. Batman probes the Cadmus conspiracy to destroy the Justice League.

A team of supervillains dubbed "Task Force X" (better known in comics as the Suicide Squad) composed of Deadshot, Plastique, Captain Boomerang, and the Clock King is recruited by Cadmus. They steal the Annihilator armour from the Watchtower.

Felix Faust, imprisoned in a mirror, fools Tala into letting him out, whereupon he possesses the Annihilator and casts Hades out of Tartarus. After her armor and lasso's full powers are activated by Hippolyta, Wonder Woman teams up with Hawkgirl to help Hades reclaim his kingdom at Zeus's command. Meanwhile Wonder Woman and Hawkgirl must deal with their anger towards each other following the events of "Starcrossed".

Huntress is kicked out of the Justice League for attempting to murder mob boss Steven Mandragora, the man responsible for her parents' death. She recruits the Question to assist her in finishing him off while Green Arrow and Black Canary attempt to thwart their efforts.

Lex Luthor's candidacy for president moves forward as Captain Marvel appears to endorse his candidacy. Luthor expertly manipulates Superman's mistrust, tricking Superman into fighting Marvel. Superman was humiliated after knowing that the bomb he defused turned out to be a generator. At the end, it is revealed by Batman that Superman had been baited by Luthor and Amanda Waller to discredit the JLU.

When the Justice League receives a distress call, Hawkgirl, Vigilante and Vixen investigate only to find that it was a trap set out by the remaining Thanagarian warriors who blame Hawkgirl for their loss in the war (as recounted in "Starcrossed"). Likewise, Hawkgirl has to deal with her teammates' resentments for her betrayal of the Justice League and her own, still-lingering self-doubts.

After helping Superman defeat Mantis, Captain Atom's Air Force Reserve commission is reactivated. Meanwhile, the Question discovers the records about the Justice Lords, and Luthor's attempts to discredit the Justice League. The Question is captured, and Superman and Huntress attempt to rescue him. Almost successful, they are confronted by Captain Atom, who has orders to stop them.

Lex Luthor seizes control of the Watchtower's main gun to fire on Cadmus, causing massive collateral damage on the city and falsely implicating the League as responsible. Convinced it is an act of revenge, Amanda Waller commands Galatea to attack the Watchtower with an army of Ultimen clones.

The founding members of the Justice League, with the exception of Batman, surrender to the government. In the middle of a huge battle between the "Unlimited" part of the League and the army of Ultimen, Supergirl and Steel battle Galatea to keep her from destroying the Watchtower.

With most of the League unavailable, the League's original seven battle against the fused Luthor and Brainiac. It is then up to the Flash to stand up against the Luthor-Brainiac team, and he is prepared to pay the final price. In desperation, Flash pushes his powers to their limit, running as fast as he can around the world numerous times and tapping into the Speed Force in order to separate and defeat the two villains. As a result, Flash is very nearly pulled into the Speed Force, but is rescued by the teamwork of his teammates. The incident leaves Flash with the disturbing possibility that traveling that fast again might mean he would never come back.

In the future of Batman Beyond, Amanda Waller reveals to an older Terry McGinnis she created the project Batman Beyond to continue Bruce Wayne's work.