Safely secluded in an undersea crevice, the Manta-Sub lies in waiting. In the brig, Lagoon Boy slings insults at Aqualad for his betrayal. Aqualad does not respond. They are interrupted by Black Manta, who demands the prisoner to be brought to the Partner immediately. Aqualad offers to do it himself, but his father has another task for him. Lagoon Boy insults him again, at which Aqualad coolly replies that he knows his place. He injects a sedative into La'gaan's bloodstream, which causes him to pass out. He is placed in a pod and carted off. Black Manta explains that though he trusts his son completely, the Light requires more evidence.
The Manta-Flyer departs. For his mission, Aqualad has assembled a strike team consisting of Icicle Jr., Tommy Terror, Tuppence Terror, and his new right hand, Tigress. Tuppence has some doubt in Aqualad's allegiance, as in their last encounter, he tried to arrest the twins. Tommy thinks the change of heart is because Aqualad found his true father. Icicle jumps in on the conversation and tells them it's because of a girl, which he sympathizes with. He takes the opportunity to hit on Tuppence, but she brushes him off. Tommy is not concerned about Kaldur'ahm—he knows next to nothing about Tigress, and doesn't trust her. Tigress rebuffs him by asking if they all want to challenge Black Manta's trust in his son and herself. They stay silent, apart from Icicle, who again tries his luck with Tuppence, this time recounting how Miss Martian impersonated her and he fell in love with that. Tuppence gives him the cold shoulder. Kaldur urges them all to focus on their mission.
Jaime Reyes answers the doorbell, and is surprised to see Impulse. Bart wants to hang out, but Jaime is afraid it might cost him his secret identity. To avoid the possibility of people seeing them together, he changes into his armor and they head out of town.
On her way to the lab, Karen is lost in her book. She doesn't notice Mal, and is surprised when she bumps into him. He wants to take her out for the night, as they haven't seen each other in a while. He quickly rebuts her response by saying mission briefings—like the one the night before—don't count. Karen accepts a date, but she needs to work in the lab first. He offers to keep her company. She accepts, but warns him he'll be bored.
Two Manta Troopers bring Lagoon Boy's pod to the Partner. Two aliens discuss what to do with him; the first sees no use for him. The other argues that, because Atlanteans are evolved from Humans, and evolved into several subspecies, it might be worthy of research—the Meta-Gene might be involved.
In the mountains outside El Paso, Blue Beetle and Impulse show off. Blue Beetle uses his sonic cannon to destroy several large boulders, and challenges Impulse to top it. Impulse doesn't go for destruction, instead, he picks up the chips and whizzes around the plain. The scarab is not convinced by this work, but Impulse explains his friend needs to look at it from a little higher. Jaime sees what Impulse made: a self-portrait in lines of pebbles. But before he can come down, he is surprised from behind. Tuppence Terror slams him to the ground. Impulse notices she is not alone. He narrowly escapes the charging Tigress, but bumps off Tommy Terror. Tigress shoots a bolt with a net at him, pinning him to the ground. Tommy helps his sister restrain Blue Beetle, so Icicle can encase him in ice. Kaldur watches from a ledge.
Both of them break free, and Blue Beetle knocks out Tommy and Icicle with his sonic cannon, and pins Tigress to the ground with a staple. He blasts the charging Tuppence from close range, sending her flying as well. Impulse joins him. The Scarab suggests eviscerating their enemies, but Jaime opts for a strategic retreat. Impulse won't go without seeing Kaldur. He hurries over to the ledge, where Kaldur still stands silently. Impulse avoids a few blows, and makes off with the alien tracking device he used to track Blue Beetle. They escape their attackers; Kaldur does not pursue. Tommy berates Kaldur for letting the two of them escape, with the tracking device.
Impulse and Blue Beetle arrive at the Cave, where Nightwing meets up with them. He wants to know about what happened, and is not pleased the two of them brought foreign, possibly alien technology inside the mountain. He takes the device from them.
Aboard the Manta-Flyer, Aqualad has another tracking device, and explains to Tommy that it is actually more. It tracks the other device, which served as a Trojan horse and disabled Cave security. The Flyer lands and submerges close to Mount Justice.
Kaldur enters the mountain through the hangar. He is met by Sphere, who does not take any action and rolls back.
Two alien sentries bring Lagoon Boy's pod to a lab, where a female scientist is waiting for him. As she turns away, he sees he is not alone: Shimmer, Tye and several other kids are stored in pods just like his.
Just like Karen predicted, Mal is bored. He plays with his cell phone while Karen is working with her microscope. Mal suggests heading to the Happy Harbor Bowl-o-Rama, but he didn't know it closed down months earlier. He laments the good times they had there together. Doctor Palmer enters the lab, and greets his guest. Karen alerts him to what's under the microscope. Palmer is impressed, and suggests additional testing. Karen already has the test prepared. When he hears it will "only" take two or three more hours, Mal leaves.
Wolf sleeps on the couch in the lounge. He is briefly distracted by a strange scent, before going back to sleep. Tigress comes out of the extractor hood and locks an inhibitor collar around his neck.
In his room, Gar watches Hello, Megan! when he is disturbed by a knock on the door. He answers it, but is immediately punched in the face by Tuppence.
Superboy is in the Grotto, looking at Artemis's statue. With his super hearing, he notices an intruder. He avoids an ice blast from Icicle, but Tommy hits him head on. Icicle encases Superboy in ice, but it doesn't stop him. He breaks free, but Tommy immediately puts an inhibitor collar around his neck. Icicle brings him to his knees by activating the collar. Both of them want to kill Superboy, but Kaldur orders them not to.
Nightwing is still in the Mission Room with Impulse and Blue Beetle, analyzing the tracking device. A small alarm goes off, at which Nightwing exclaims he is an idiot and takes out his eskrima sticks. Before he can do anything, Superboy is tossed into him and he is pinned down. Icicle blasts the floor with ice, but Impulse sees through it. He goes around, up the wall, and body checks him. Seeing Tuppence with Beast Boy, he tries to do it again, but she's too strong. He bounces off her, straight in the hands of Tommy, who fits a collar around his neck. Impulse thinks he can vibrate out of it, but finds his powers are blocked. Tommy knocks Impulse to the floor and Blue Beetle attacks with his sonic cannon.
Nightwing gets up again, but Tigress is onto him, and fits him with a collar as well. As it does not affect him, he throws Tigress off of him. She responds by activating the taser, which knocks him out. Blue Beetle wants to attack everyone, but Kaldur persuades him not to, by bringing in a bomb. The bomb, of similar design as the one that destroyed Malina Island, will go off if Kaldur removes his thumb from the dead man's switch. The scarab argues that it is a bluff, and if not, they will likely survive the blast, but Jaime stands down as his friends cannot. He too gets a collar, and Kaldur orders Icicle to escort the prisoners out. As a parting gift, he punches Nightwing in the stomach, and warns him not to pursue.
On the beach, the Scarab informs Jaime he can disable the inhibitor collar. Jaime refuses, but the Scarab usurps command. He knocks out Tigress and Icicle, and blasts Kaldur, who drops the switch. It was a bluff. Blue Beetle charges at him, but Kaldur defends with a blast of magic at point black range. It blows a hole in the armor, allowing Tigress to shoot a sedative dart at him. He passes out, and is carried aboard.
As the Manta-Flyer takes off, Tommy and Icicle question Kaldur's resolve, and suspect he still has a soft spot for his former teammates. Kaldur retaliates by ordering Tigress to detonate the bomb. She takes off her mask to ensure he's absolutely certain, and he insists. She pushes the detonator.
In the Mission Room, the bomb goes off. It creates an explosion that takes out the entire mountain. Beast Boy and Impulse watch in shock.
In the streets of Happy Harbor, people witness the explosion and are perplexed. Mal, fresh from Ivy Town, is equally shocked. He calls the Watchtower for assistance, and heads out to the mountain to see if he can find anyone. He detects the presence of the Super-Cycle, and finds her in the water, with Nightwing, Superboy and Wolf. He swims out to them, and grabs a hold of Nightwing. He wakes Superboy, who carries Wolf. The cycle curls up into her ball mode and falls to the ocean floor to heal. Mal and Conner swim to shore.
Wally arrives in the Hall of Justice, where Nightwing is recuperating. He is angry with his friend, who insists it was necessary to cement Kaldur's place, and allow him to pass on information to Lagoon Boy's whereabouts. Wally is not convinced—three more members of the Team are captured, and people very nearly died. Plus, "killing" Artemis was supposed to be enough to make Kaldur's cover safe. Wally doesn't care about the Cave as much as he does about Artemis. He also expresses the concern that Aqualad may be, in fact, a triple agent. He lost the love of his life and discovered his true parentage in the span of months; it could easily have driven him over the edge.
The Manta-Flyer docks with the Manta-Sub, and the strike team boards the larger vessel. Manta Troopers unload the prisoners, and Black Manta commands his son to come with him. He leads him to his private quarters, where on video screens, the members of the Light appear. Black Manta introduces Kaldur'ahm to them, and Ra's al Ghul takes the word. He is pleased with the results, and appreciates vision, initiative and strong family ties. Kaldur is fully welcomed into the Light, and prepared for a meeting with the Partner.
The title of this and the following episode is taken from the saying "It's always darkest before the dawn", or other variations. Metaphorically speaking, two "dark" things occur: the abduction of Impulse, Blue Beetle and Beast Boy, and the destruction of Mount Justice. Also, these events take place during nighttime.