Episode 3: Alienated
Takes place on January 5 - 7, January 26
Miss Martian returns to Earth and shares what she has learned. The Kroloteans try to build a spaceship to leave Earth (since the Zeta beam transport has been disabled) at a secret island base with help from Black Manta's son. The base is found and attacked by Batman, Aquaman, Superman, Wonder Woman and Martian Manhunter along with their respective sidekicks. Manta's son is revealed to be Aqualad, who is bitter that Aquagirl was killed and that Aquaman never told him who his actual father was. A Time Bomb (set by the Kroloteans' mysterious competitors) forces everyone to escape (except the Kroloteans, who die for refusing to believe Superman).
In the end, the six Leaguers who attacked another planet while under The Light's control must leave Earth to face a trial. Black Manta officially joins The Light, filling the position left by Ocean-Master.
- Bibbo Bibbowski, the restaurant owner from the first part of the episode, is a minor character from Superman comics.
- It is revealed that the Justice League came together to repel an Appelaxian invasion, as in the Year One comic. Several host bodies are currently on display in the publicly accessible portion of the Hall of Justice.
- The Krolotean pursued by Blue Beetle and Bumblebee claims to have been attacked by an agent of the mysterious "Competitor".
- Other exhibits include the armor of Guardian, a dismembered Amazo, and what appears to be Katana's katana.
- Tula joined the Team as Aquagirl at some point during the 5-year gap, only to later be killed during a mission.
- We see a growing embitterment towards the Justice League from the media.
- Wonder Girl is revealed to have a mother, and may be living with her.
- Wonder Girl's mother, Kaldur being Black Manta's son, and the death of Tula are all featured in Young Justice: Legacy, set about a year before season 2.