In her quarters aboard Black Manta's sob, Artemis worries about the complications that have arisen since she is working undercover disguised as Tigress, a villainess. She looks at her own face in the mirror, stripped of Zatanna's glamor, and admits that she gave up her home life with Wally for the thrill of an undercover assignment. Black Manta calls her to Aqualad's quarters and tells Artemis that that he has brought in Psimon to cure Aqualad after his mind was destroyed by Miss Martian's telepathic attack. When Psimon boasts that he will learn everything in Aqualad's mind, Artemis realizes that she has to do something before he learns about Aqualad's undercover assignment... and hers. Psimon says that he'll need time to meditate and prepare, and Black Manta assigns Artemis to guard him while he goes to get revenge on Miss Martian.
At Taos, Miss Martian hesitates to ready Green Beetle's mind while the rest of the team looks on. Her fellow Martian says that's it okay, but Superboy worries that it could be dangerous. Nightwing says that it's their only option and Lagoon Boy assures his girlfriend that everything will be all right. Miss Martian begins and Green Beetle reads her mind and learns that she's a White Martian. He realizes that she reluctantly injured someone with a telepathic attack and is reluctant to probe deeper, so he opens his mind to her. Miss Martian finishes her scan and says that Green Beetle checks out.
Once he finishes meditating, Psimon begins scanning Aqualad's mind. Artemis secretly shoots him with a drugged dart and he soon starts to feel the effects. Psimon telekinetically slams Artemis around the room and Black Manta sees the attack on the monitors. As he goes to the room, Psimon realizes that Artemis is an undercover agent and that she injected him with a drug developed by her father Sportsmaster to render a victim comatose. He passes out just as Black manta comes in, and Artemis plants a seed of doubt by saying that Miss Martian must have left a telepathic virus in Aqualad's mind. Black Manta takes the bait and realizes that any telepath they bring in could suffer the same fate. Artemis suggests that she abduct Miss Martian and bring her to undo the damage she did, and Black Manta agrees. However, the villain orders her to take The Light's enforcer, Deathstroke, with her.
Green Beetle analyzes The Reach's energy drink and informs Young Justice that it contains a drug that will render Earth's population placid and ripe for conquest. Nightwing tells the Martian that they already confirmed that and Green Beetle realizes that they were testing him. However, he also confirms that there is an element they didn't identify that lets The Reach identify and harvest the meta-gene among Earth's population. Impressed, Nightwing offers to pass on the information to the League but admits that there's nothing they can do about it immediately since Godfrey has been destroying the League's credibility. As the team leaves, Green Beetle uses his shapeshifting abilities to take on human form and says that he'll make a life for himself in Taos. Lagoon Boy asks to talk to Miss Martian privately and she glances over briefly at Superboy before agreeing to go to her uncle's apartment in Chicago where she's living. Meanwhile, Impulse tells his friend Blue Beetle that they should go out but Blue Beetle turns down his offer.
Miss Martian and Lagoon Boy take the Zeta Beam teleporter to a junkyard in Chicago. Lagoon Boy wonders what's going on between her and Superboy. However, Deathstroke and Artemis attack before she can answer. Miss Martian establishes telepathic contact with Artemis, who privately explains that she's been sent there to kidnap her so she can help Aqualad. Artemis wants Miss Martian to play along but make it look good so that they fool both Deathstroke and Lagoon Boy. Meanwhile, Lagoon Boy calls for backup and Nightwing says that they'll be there in three minutes. Deathstroke subdues Lagoon Boy in his giant form, breaking his leg and punching him unconscious. Meanwhile, Artemis uses fire bombs on Miss Martian, weakening her so that Deathstroke can put an inhibitor column on the heroine. They depart in a Manta ship just before Nightwing and Superboy arrive.
Blue Beetle and Green Beetle walk into Taos to find a place for the Martian, and Jaime explains that he can control the scarab. However, he's worried that it could take full command of him and turn him into an agent for The Reach. Green Beetle offers to teach Blue Beetle meditation techniques to control the scarab, but admits that he used his shapeshifting abilities to alter his body and cut off the scarab. When Blue Beetle asks him to do it, Green Beetle warns that it could kill him but Blue Beetle says that he'll do anything to be free of it.
Miss Martian wakes up aboard Black manta's sub and the villain tells her to repair Aqualad's mind. Deathstroke will monitor her from outside of her mental range and detonate a bomb in the collar if she does anything suspicious. They activate her telepathic abilities only and leave, putting Artemis on guard. Miss Martian tells her friend that she doesn't know how to fix the damage she caused and worries that Aqualad may sense her presence in his mind as a threat. Artemis offers to go in with her since Aqualad will accept her and Miss Martian accepts. They find themselves inside of a mindscape filled with the underwater ruins of Atlantis. Artemis begins to drown until Miss Martian reminds her that everything is in her mind and can only work if they let it. Once Artemis recovers, Aqualad's dead girlfriend Tula attacks them with her water powers, blasting the two of them back.
Nightwing and Superboy take the injured Lagoon Boy to the hospital. He insists on going back out to find Miss Martian and blames Superboy for abandoning her to Tigress. Superboy angrily says that Lagoon Boy knows nothing about him and Nightwing reluctantly tells them that Tigress is Artemis, working undercover to infiltrate The Light along with Aqualad. Lagoon Boy complains about being kept in the dark but Superboy supports his leader. However, once they're outside and alone, Superboy points out that Nightwing has endangered all of their teammates by keeping secrets. Miss Martian only damaged Aqualad's mind because she didn't know that he was working undercover. Now Black Manta has captured Miss Martian and will kill her if she can't repair Aqualad's mind, and Miss Martian doesn't know how to fix the damage.
The mental image of Tula continues attacking Miss Martian, who is too filled with guilt to resist. When she realizes that she can't do anything against the projection, Artemis swims off and finds a faceless Aqualad sitting among the ruins. He insists that Aqualad is no longer there and a vortex forms nearby, pulling the wreckage in. Artemis holds onto him and insists that they need to work together if they want to put his mind back together.
Tula defeats Miss Martian, who insists that she deserves to die. Artemis arrives with a partially restored Aqualad and tells Miss Martian that she needs to fight back so that she can make amends. Miss Martian apologizes to Aqualad and insists that they need to work together. Aqualad begins to focus and the scattered ruins slowly begin to assemble themselves...
Black Manta wakes up Artemis, who has been staring into space for the last six hours. Miss Martian also comes out of her trance and tells them that it may take months for her to repair all of the damage. Black Manta accuses her of stalling, but Aqualad comes out of his coma long enough to call for his father. He accepts that she's doing her best and tells her that she'll live as long as she makes progress. However, outside Black Manta tells Artemis to kill Miss Martian once she's done her job.
Impulse speeds up to Green Beetle and Blue Beetle and discovers that the Martian has inserted his shapeshifted hands into Jaime's scarab. As Green Beetle withdraws, Blue Beetle tells his friend that they've cut off the scarab and he is now in control.