Jaime Reyes is skateboarding home at night past Kord Industries. An explosion rocks the building and a piece of debris lands on Jaime's back. He quickly rips off his shirt and finds a blue scarab-shaped object on the ground. When he picks it up, It crawls onto his back and enshrouds him in blue armor.
Jaime wakes up from his dream and finds himself in a pod in the alien base somewhere in the Pacific Ocean. The Scarab, still linked to him, complains that Jaime let them be captured and informs its host that the neutralization system prevents it from armoring up. Two aliens, the Scientist and the Ambassador, briefly examine Jaime and the Scarab translates for its host. They have discovered that the Scarab's memory files have become corrupted and it only remembers everything in the last eight months since it fused with Jaime. The Ambassador orders the Scientist to perform a reboot but she wants to study the problem so they can avoid it in future. A figure dressed in a black version of the Blue Beetle armor steps out of the shadows and points out that the Scientist just wants to play with it.
Later, Aqualad visits the Ambassador's ship. The Ambassador gives their new ally a tour and explains that they call themselves the Reach. They are performing research on the human meta-gene, a trait that lets humans adopt to crisis by developing superhuman powers. The Ambassador introduces Aqualad to the Scientist and she thanks him for providing test subjects. Among the captives are Lagoon Lad and the Scientist explains that besides studying meta-humans, they are trying to trigger the meta-gene in non-superpowered individuals. Lagoon Boy has no superhuman abilities.
In the next lab, the Scientist shows Aqualad her stress experiments on individuals with activated meta-genes, heroes like Impulse and Beast Boy. She plans to see if her abilities can be extracted and duplicated. The Scientist goes into the third lab but the Ambassador refuses to grant Aqualad access. He comments that Blue Beetle is inside but that he is of the Reach and of no concern to Aqualad. Aqualad assures the Ambassador that his best operative is providing the next batch of test subjects.
In Star City, Bumblebee, Tim Drake, and Barbara Gordon approach the dock where Artemis--still undercover as Tigress--has collected local teenagers. The heroes land inside the containment cage and blend in as Black Manta's start removing teens and placing them in pods. A flyer arrives and the troops load the pods aboard it and depart. Nightwing, Wonder Girl, and Miss Martian follow it in the latter's cloaked bioship.
While Jaime fades in and out of consciousness, the Scientist analyzes his Scarab and wonders why it won't function. Black Beetle tells her to reboot and she warns that they'll need a new host. Her partner assures her that they can easily find another host but the removal process will kill Jaime.
The flyer arrives at the Reach's underwater ship and Nightwing realizes it matches the alien design of the bomb that destroyed Melina Island. Miss Martian goes invisible and intangible and enters the base, establishing mental contact with Barbara. Barbara describes the interior and warns them that Aqualad is present. Miss Martian finds the missing heroes as well as the villain, Shimmer. Nightwing tells them to wait even before they find Blue Beetle. Miss Martian frees Beast Boy and Impulse and the latter immediately speeds off to find Jaime, setting off alarms.
As Artemis goes to check the alarm, one of the troopers throws her aside and attacks the other troopers. Superboy then removes his helmet and meets with Barbara and the other freed teens. Nightwing and Wonder Girl dock the ship while Barbara and Tim fight a holding action.
Miss Martian and Beast Boy find Aqualad and the Martian launches a telepathic attack on her former teammate, driving him to his knees.
When Superboy realizes that he's lost his link with Miss Martian, he goes to find her but Black Beetle knocks him back and seals the docking chamber. Wonder Girl suggests that he surrender but he laughs and switches to full battle mode.
Impulse continues his search, vibrating through walls until he knocks out the Scientist and frees Jaime.
Miss Martian scans Aqualad's mind and sees everything he's done, including working undercover with Nightwing and faking Artemis' death. Artemis arrives and Miss Martian telepathically explains that she thought Aqualad deserved her anger because he killed Artemis. Beast Boy, unaware of what's going on, attacks Artemis and she escapes using a smoke bomb.
Black Beetle easily knocks aside the heroes and one of the trapped teenagers grabs a weapon. Shimmer knocks him down and Black Beetle nods in satisfaction as Superboy and Wonder Girl return to the attack.
Impulse tells Jaime about how the Reach gets him online and turns him into a weapon to dominate the humans of the future. Jaime insists that he wouldn't but Impulse says that he does and that's the real reason that he came to the past: to stop him from betraying the human race.
Miss Martian arrives with Beast Boy and telepathically contacts the heroes trapped in the docking bay. Nightwing warns that he's cut off from the bioship. Miss Martian manages to focus and slip through the door. Black Beetle touches the door, shifting its density and stunning her. He slams Wonder Girl into the door repeatedly until she passes out. Blue Beetle gets the door open and opens the door on the opposite side. Black Beetle warns his counterpart that he can't escape the Reach, and the Scarab asks for total control of all weaponry. Jaime agrees and attacks Black Beetle.
Barbara appraises Nightwing of the situation and tells him to pilot the bioship out once she and the other heroes get all of captives onboard.
The two armored figures pound away at each other while Shimmer touches the wall and discovers that her enhanced powers have transformed it into air, flooding the base. Everyone else gets aboard the bioship and Impulse is unable to go back against the rising water pressure. Nightwing pilots the bioship away while inside, the two Beetles blast at each other. The backlash knocks Blue Beetle out through the hole and Black Beetle seals the breech and activates the ship's weaponry. Lagoon Boy grabs Blue Beetle and gets him aboard the bioship as it escapes the area.
Blue Beetle comes back online and assures everyone that he's himself. Nightwing notices that Miss Martian is still extremely passive and Beast Boy tells him that she telepathically defeated Aqualad. Superboy, remembering his ex-girlfriend's efforts to tamper with his mind, glares at her. Nightwing reports to Aqualad and Captain Atom at Watchtower, telling them that the aliens have been exposed. However, reporters are already commenting on the arrival of a Reach ship at the UN. G. Gordon Godfrey explains that Earth has met friendly aliens as the Ambassador offers his people's assistance to anyone who wants it. Nightwing realizes that the aliens have gone public to avoid bad publicity when the League reveals their existence. However, the heroes are confident that they now know what they're up against.
At the Marianas Trench, a fleet of Reach ships emerge.