Five years have passed since season one, bringing drastic changes, including many alterations to the line-ups of both the Team and the Justice League.
Public perception of super-heroes takes a turn for the worse, thanks in particular to the GBS commentaries of G. Gordon Godfrey.
The heroes discover what occurred over the missing 16 hours, during which six Leaguers were under Vandal Savage's mind control. As a result, those same Leaguers leave Earth to undergo a criminal trial on Rimbor.
Multiple aliens have secretly invaded the Earth, operating there for unspecified purposes that include abducting and experimenting on humans.
The Light is still active and is now working with a new Partner (or two).
Having nearly been consumed by his five year search for Speedy, Red Arrow finally finds the original Roy Harper with the help of his estranged wife Jade Nguyen, who also introduces Clone-Roy to their daughter Lian Nguyen-Harper. Together, they bring Speedy back to Star City.
Aqualad is on a deep cover mission for Nightwing, posing as the loyal lieutenant of his father, Black Manta. As part of this mission, Artemis's death is faked and Mount Justice is destroyed, all to advance Aqualad's credentials with Manta, the Light and their Partner.
Sportsmaster and Cheshire vow vengeance on Aqualad and Black Manta for the 'death' of Artemis, when in fact, Artemis has gone under cover as Tigress.
In a paroxysm of anger, Miss Martian puts Aqualad in a catatonic state, before finding out that his betrayal and Artemis's death were staged.
The Reach makes themselves known to the public, professing good intentions, but all the while concealing a hidden agenda.
The Reach manufactures food for human consumption with eerie purposes.
The abductees manifest superhuman abilities and are recruited by Lex Luthor.
Learning from Impulse that he will bring upon an apocalypse, Blue Beetle is determined to remove his scarab.
Sportsmaster defects from the Light and pursues his vendetta against Black Manta and Aqualad with Cheshire. Deathstroke takes his place as the Light's enforcer.
A new Beetle appears, pretending to be an ally of the heroes, and offers to help Blue Beetle to take control of his scarab. However, it was all an elaborate ruse, as he is actually an agent of the Reach and manages to put Jaime under the control of the Reach.
Miss Martian is kidnapped at the behest of Black Manta and coerced to fix Aqualad.