In Metropolis, Blue Beetle and Bumblebee in their civilian identifies go into a diner where the owner, Bibbo, is watching one of G. Gordon Godfrey’s televised rants against aliens. Bibbo stares at them, panics, and runs out the back, and the two heroes give chase. The real Bibbo steps out and punches his duplicate, revealing that he’s a Krolotean android impersonator. The alien flees into the sewers before Bumblebee can stop him and escapes in an emergency vehicle, covering his escape in a back blast. Blue Beetle argues with his armor about what he should have done, while Bumblebee and Bibbo stare at him.
The Krolotean escapes into Metropolis Bay where Black Manta is waiting in his Manta Sub with more Kroloteans. They submerge and depart the area.
In Taos at the STAR Lab facility, Nightwing and several League members wait as Adam Strange and the Young Justice team return from Rann by teleportation beam. They report that their mission was success and Adam shows them the teleportation shield that will keep more Kroloteans from arriving on Earth. Miss Martian telepathically shows the others what happened on Rimbor. The Kroloteans paid off a Rannian general to land secretly on the planet, stole Sardath’s technology, and used the platforms to beam the Kroloteans to Earth. From there they have been abducting and replacing humans, but Miss Martian isn’t clear why.
During the missing sixteen hours, Vandal Savage sent the six League members to the planet Rimbor to go on a rampage attacking everyone in sight and loudly announcing that the galaxy should beware the Justice League. The Kroloteans heard of the incident and invaded Earth as a result. John Stewart heads to Oa to consult with the Guardians and the Green Lantern Corps to find out why nobody reported the incident.
At the Hall of Justice, Catherine Cobart is taking a tour group through the exhibition hall. Some of the crowd discuss Godfrey’s suspicions about aliens but Catherine ignores them and continues. Deeper into the building, Miss Martian and Superboy go to the interrogation room with Batman, where Martian Manhunter is telepathically interrogating the Krolotean that Lagoon Boy and the others captured. Miss Martian telepathically scans the Krolotean herself and immediately tells Batman that the aliens have an emergency rendezvous point inside a volcano on Molina Island.
The Black Manta who rescued the Kroloteans arrives at the island, where the others are building a ship to escape Earth. The real Black Manta is there and congratulates his son, who is wearing his costume. The son removes his helmet, revealing that he’s Aqualad.
Batman, Batgirl, Nightwing, Robin, Aquaman, and Lagoon Boy secretly approach the island and drop Aquaman and Lagoon Boy off. As they enter via the underwater entrance, Batman and the others land and go in, taking out the guards. Inside, the Kroloteans finish their work on the ship and discuss how “the Competitor” is the one who hired Lobo to attack and reveal them.
Aqualad prepares for Phase 2 and notices that one sector is failing to report. Meanwhile, Aquaman and Lagoon Boy monitor the cave from below while the Bat team moves in from above. Aqualad realizes that they have intruders, notifies his guards, and opens fire. The heroes engage while the Kroloteans activate their mechs and try to activate the ship. Unseen, another figure moves in and penetrates the security systems.
Aquaman goes after Aqualad, who blasts him back with a laser beam. He then calls his partner and says that the base has been infiltrated so they should abort their operation. The partner says that the self-destruct has been activated and Aqualad has five minutes to get his men out. Nightwing spots their retreat and calls in backup from Superman, Superboy, Wonder Woman, and Wonder Girl. The Kroloteans download their information, while Aquaman and Lagoon Boy attack Aqualad together. They knock off his helmet and realize that he’s Aqualad. Aqualad angrily reminds them that they let Aquagirl die and Aquaman hid the knowledge of his true father, Black Manta, from him. He refuses to be consoled and fires a missile, providing a distraction to escape. Nightwing and Superboy catch up to him and he tells them that they can capture him or stop the bomb, and they have two minutes. He dives into the water while Nightwing checks the bomb and realizes that he can’t defuse it. He tells the others to get out and they begin their retreat.
Superman tries to get through to the Kroloteans and warn them about the bomb, but they view the retreat as a victory and open fire on the Kryptonian. Meanwhile, Miss Martian and Martian Manhunter pick up the others in the bioship. As they fly away, the bomb explodes, wiping out the island. Superman is knocked into the ocean and the team picks him up. Superboy warns that he won’t be okay with the destruction of the Kroloteans. Nightwing reports that the bomb was of alien origins and they don’t know where it came from, and Batman says that Young Justice may have to find out.
Aqualad reunites with his father, who is disappointed to learn that Aquaman didn’t die in the explosion. Black Manta is called away to meet with the Light’s council. Vandal Savage informs him that their ally, the Competitor, is pleased with Black Manta’s efforts as is the Light since he has replaced Ocean Master. They proclaim Black Manta one with the Light.
At Mount Justice, the six accused League members prepare to leave to defend themselves before the High Court of Rimbor based on the Guardians’ advice. Superman assures Superboy that he will be back, and Martian Manhunter asks Miss Martian to water the plants in his apartment while he’s gone. Nightwing assures Batman that they’ll manage in their absence and the League departs.