Endgame

June 20: The council of Rimbor has finally made its decision and declares the Justice League to be guilty. Superboy and Miss Martian show up with new evidence, but are told that it is too late. Back on Earth, Aqualad and Blue and Green Beetle take on Black Beetle on board the Reach ship. Black Beetle destroys Green's scarab, but Blue destroys Black's. However, he learns that Black Beetle has set an endgame in motion. Back on Rimbor, the council reconvenes and after some persuading, agree to reassess the case, and eventually release the League.

Around the world, twenty Reach devices begin to damage the Earth's magnetic field, causing various types of natural disasters. Every hero is called in to split into teams of two, each duo carrying one of twenty devices provided by Lex Luthor that will shut down the machines. They succeed, but Jaime discovers a twenty-first machine in the Arctic. Flash and Impulse arrive to find that it has already gone into "chrysalis" mode and will soon destroy Earth; the two, directed by Luthor, use their speed to create a vortex that draws off the device's energy but need a further boost in order to succeed. They are soon joined by Kid Flash, but Wally's slower speed makes him a target for stray energy discharges which apparently cause him to disintegrate. The machine is shut down and Flash tells a distraught Artemis that Wally said he loved her before vanishing. The Justice League arrive back on Earth to be greeted by the Team, who inform them of Wally's disappearance.

July 4: The world is finally free of the Reach, who are set to face trial for their actions. Blue Beetle watches as the Reach leave, his scarab assuring him he is free, leaving him satisfied. G. Gordon Godfrey starts campaigning for Lex Luthor to replace the now-resigned Secretary General Tseng, much to Superman's dismay. Impulse honors Wally's memory by taking on the mantle of Kid Flash, as Wally had asked him to do previously, and Artemis rejoins the team as Tigress, unable to continue fighting as Artemis for the time being, stating that "Artemis was Wally's partner". Virgil joins the Team as Static, and romance blossoms between Robin and Wonder Girl as Superboy and Miss Martian begin to patch up their own relationship. Nightwing, grieving the loss of Kid Flash, takes a break from being a hero and maintains that Aqualad should remain leader for the time being with Batgirl as his assistant. The Team are told that they will work out of the Watchtower, side-by-side with the League.

July 5: G. Gordon Godfrey and Desaad look on as Vandal Savage meets with Darkseid on Apokolips.

Mark Desmond, Bruce Wayne/Batman, Arthur Curry/Aquaman, Dubbilex, Dick Grayson/Robin, Conner Kent/Superboy, Clark Kent/Superman, Kaldur'ahm/Aqualad, J'onn J'onzz/Martian Manhunter, Wally West/Kid Flash, Oliver Queen/Green Arrow, Blue Beetle, Beast Boy, Lagoon Boy, Wonder Girl, Bumblebee, Batgirl

Season two is retitled Young Justice: Invasion, and takes place five years after the events of the first season. This continues the story of the young heroes as the team (Aqualad, Kid Flash, Superboy, Miss Martian and Artemis)- now led by Nightwing- and its new members (Robin, Blue Beetle, Beast Boy, Lagoon Boy, Wonder Girl, Bumblebee, Batgirl) go deeper and more covert than ever before. As team rivalry and personal conflicts arise, the team must band together to fight the real threat that faces Earth.