Five years later...
Young Justice has gained and lost members, and works closely with the Justice League. Now, an alien race has launched an invasion of Earth from Rann using teleporters, and only Young Justice can travel there since the Justice League has been outlawed on the planet.
On Rann, Beast Boy, Miss Martian, and Superboy team up with Adam Strange to locate the home base of the Kroloteans and stop the invasion at its source.
Young Justice and the Justice League track down a major Krolotean base on Earth and launch an attack, only to discover that an old ally is assisting the alien invaders.
Superboy and Blue Beetle go after Bruno Mannheim of Intergang, believing he was involved with the destruction of Malina Island. Meanwhile, Nightwing and several of his teammates track down the Roy Harper clone and try to convince him to set aside his quest to find his progenitor.
While a team of female Young Justice members enter Bialya to track down the alien tech used to destroy Malina Island, Blue Beetle looks for a missing friend in El Paso.
Impulse, a speedster from the future who claims to be the Flash's grandson, arrives at Mount Justice and is eager to meet his relatives. Meanwhile, Red Arrow and Cheshire track down Roy Harper.
Nightwing calls Artemis back into action to defend a comsat launch against enemy saboteurs. But the team soon discovers that another old teammate has also returned... and is willing to do whatever it takes to stop the rocket.
While Young Justice go on with their lives, Green and Red Arrow explain to the recently-discovered Roy Harper that he has been a prisoner for eight years after being cloned, and he sets out to take revenge on the man responsible.
To prove his loyalty to the Light, Aqualad takes a team of villains on a mission to capture members of Young Justice... and destroy their headquarters.
The team goes on a mission to rescue its missing comrades, and discovers that the Reach is allied with the Light and responsible for the abduction of dozens of teenagers... and plans to use Blue Beetle to further their invasion plans.
Young Justice's relocation after the destruction of Mount Justice is interrupted by the attack of an alien gladiator. Meanwhile, Black Canary interviews the Reach abductees, and the Reach ambassador continues to undermine the League's standing on Earth.
The Reach claims to be helping Earth with its agricultural problems and forms an alliance with LexCorp. Suspecting the worst, Nightwing sends an undercover team in to gather samples and determine what The Reach is really up to.
Black Manta seeks revenge on Miss Martian for her telepathic attack on his son, but soon discovers that she's her only hope of restoring his son's mind. Meanwhile, Young Justice tests their new ally, Green Beetle, and Blue Beetle seeks a way to control his scarab.
Four of The Reach's teenager abductees break out of STAR Labs when they grow tired of the endless experiments on them. When Blue Beetle tracks them down, however, they agree to go back only find the lab under attack by a killer android.
Rather than let Earth fall under the control of The Reach, the alien warlord Mongul brings his planetary-sized mobile weapons platform to destroy the planet. To stop it, Young Justice and the Justice League must join forces to stop it... and receive help from an unexpected ally.
Cheshire and Sportsmaster break into Black Manta's sub to take revenge on the people they hold responsible for Artemis' death... unaware that Artemis is alive and working with Aqualad and the captive Miss Martian.
Luthor convinces the former Reach test subjects to sneak aboard Warworld and rescue the captive members of Young Justice... providing a distraction so that The Light can recover a vital piece of equipment. Meanwhile, public opinion about The Reach begins to change.
After capturing Blue Beetle, the Young Justice team takes him to Bialya in a desperate attempt to free him from The Reach's influence.
The Light and The Reach meet to resolve their differences, only to discover that Aqualad has set both sides up.
Young Justice defeats Black Beetle and The Reach, but discover the aliens' failsafe plan... to destroy Earth. Meanwhile, the Leagues face justice on the planet Rimbor.