The Team is taking Espionage 101 from Captain Atom. Their class project is to solve a cold case that involves a forty-year-old murder mystery, a military conspiracy and a half-decent chance that none of them will come out alive.
Tagline: Captain Atom Wants YOU to Solve a Mystery!
Captain Atom is giving the Team a lecture about espionage, but most of them are bored by all the information. So instead, Captain Atom gives them a cold case from the Vietnam war: the possible framing of Air Force captain Nathaniel Adams, who was convicted in 1968 for the murder of general Clement Lemar. however Captain Atom received a very reliable tip that Adams was in fact innocent. The Team accepts the terms and conditions of this new mission in order to avoid returning to the lecture.
Miss Martian infiltrates the Pentagon in the guise of a JAG lieutenant. She arranges a meeting with Wade Eiling, who was the judge at Adams's trial. Robin infiltrated the Pentagon's ventilation system and spies in on the conversation as Eiling recollects how things happened.
Adams blamed Lemar for deliberately sending him and his men into an ambush by Viet Cong. Enraged, he pulled his knife on his commanding officer. When M.P. Sergeant Polk arrived to check in on the noise, Lemar was dead. It was an open and shut case; he was sentenced to life in prison. Adams committed suicide in prison that same year.
Kid Flash and Superboy go to Vegas in civvies to question Henry Yarrow, who was previously Adams's attorney during the trial. He is more than happy to help what he thinks is a couple of journalism students, and tells them how he was told things happened.
Adams worked Air Force Intelligence, and had received information on a weapon smuggling ring. He confided with General Lemar, who agreed, and sent him and his squad to Hill 409. The squad was ambushed; only Adams and Yarrow escaped, albeit barely. Adams was convinced Lemar had set him up, and confronted him; but once there, he blacked out. When he came to, Lemar was dead and Sgt. Polk was at the scene to arrest him. Yarrow took Adams's defense in court, but all evidence was stacked against him: prosecutor Lt. Kevin Blankly showed that Lemar was murdered with Adams's knife, and medical examiner Maj. Shirley Mason ruled out Adams's story that he was drugged. The case was clear: Adams was sentenced to life in prison, where he died a year later. Eiling, the judge, married Adams's widow, and raised his two children as his own.
Yarrow says he was convinced the case was a set-up, but never had the evidence to prove anything.
Following up on Yarrow's story, Robin and Miss Martian investigate Shirley Mason, are surprised to find her dead body. They uncover a photo of her with several military officials that is on her body, they both manage to get out before the police can show up and make assumptions.
Aqualad and Artemis meet with Adams's children, Peggy and Randy. To Randy, it's clear that his biological father was a traitor, and does not like talking about him—his father is Wade Eiling. Peggy agrees with her mother, who was always convinced of Adams's innocence.
Afterward, Artemis and Aqualad discuss the two siblings, and fatherhood in general—Artemis posits that being a biological father doesn't make him the actual father, as honesty and parental skills have not much to do with biology. Aqualad does not listen; his mind is in Atlantis. Artemis asks him about his parents. His mother is Sha'lain'a of Shayeris, while his father is Calvin Durham, originally a spy of Black Manta, genetically engineered to infiltrate Atlantis. The two fell in love, and Durham abandoned his mission. Aqualad is convinced they should remain clear-headed in this case too, and not judge anyone until all the facts are in.
The Team convenes outside General Trang's mansion. Trang, a former North Vietnamese general, was on the photo Major Mason had—the only non-American on that image. Robin's facial recognition program found his data right away. Superboy spots someone beside Trang inside, who is armed with a sword. As Mason was killed by a sword, they reason that this must be the killer. Miss Martian goes in to investigate.
Trang warns his guest, Rako, that he knows what happened to Mason, and knows what he'll do to him. He is disappointed that the boy he raised since he was a child would resort to that. But as he lifts his sword, it flies out of his hand. He uses infrared glasses to find the origin, and quickly spots Miss Martian. He strikes her down, but before he can finish, Superboy bursts in. To the boy's surprise, Rako's sword is able to make a large wound in his chest.
A cold case is an unsolved crime that is being looked into decades later. It does not quite fit the issue's story, as the case the Team is working on is less of an old case that was never solved, and more of an appeal.
The croupier asks if Superboy is under 21, at which he answers if it's in weeks or in months. He was 16 weeks on July 4; by August 13, he was in his 21st week.
The writing on Aqualad's notepad during the lecture includes a "Tula" in Greek Cyrillic, and in Honolulu, Aqualad's mind drifts to his family. The events of this issue take place two weeks before "Downtime", where his homesickness is revealed.
The cover features a small bubble in the left top with Superboy; it reuses artwork from Mike Norton's cover of #0.
This storyline is based on the "Captain Atom: Top Secret" story that appeared in Captain Atom #26-28 (February–April 1989), co-written by Greg Weisman. The court-martial is loosely adapted from Captain Atom #9 (November 1987).