| Issue | Title | Writers | Pencils | Inks | Notes |
| #1 (12/96) | "Prime Directives" | Chris Cooper | Chris Renaud | Andy Lanning | Omega Squad is formed. Nog's eagerness to fit in causes a series of simulated first contact holodeck scenarios to malfunction and put the squad at risk. |
| #2 (1/97) | "Liberty" | Chris Cooper | Chris Renaud | Andy Lanning | The females enjoy some downtime in an Australian bar, while Nog gets in trouble by finding Matt's comic collection. |
| #3 (2/97) | "Loyalty Test" | Chris Cooper | John Royle | Tom Wegrzyn | Matt joins the infamous Red Squad. (This coincides with a story arc in Star Trek: Deep Space Nine where Earth defenses are put to the test when Red Squad shut off major power generators.) |
| #4 (3/97) | "War and Peace, Part I" | Chris Cooper | Chris Renaud | Andy Lanning | While tensions are high with the Klingon Empire, Omega Squad and First Cadre of the Klingon Military Academy are stranded on an uninhabited planet. |
| #5 (4/97) | "War and Peace, Part II: Love and Death" | Chris Cooper | Chris Renaud | Andy Lanning | Both teams meet and agree to a fight between two champions, the result of which is the death of Kamilah. Matt also loses his left eye in the altercation. |
| #6 (5/97) | "Passages" | Chris Cooper | Chris Renaud | Andy Lanning | Kamilah's interment, the introduction of Edam Astrun who, despite being a recluse proves he can put his skills to good use as he is recruited by Starfleet Academy for his talents as a powerful telepath. |
| #7 (6/97) | "Hide & Seek" | Chris Cooper | Chris Renaud | Andy Lanning | Nog is accused of attempted murder on Edam. The squad finds the attempt was in fact the work of a Founder, whom they chase and apprehend. Held captive, the Founder commits suicide. |
| #8 (7/97) | "X2" | Chris Cooper | John Royle | Andy Lanning | Omega Squad are held captive by Charlie X, a human child raised by aliens who gave him illusion powers, from an episode of Star Trek: The Original Series. |
| #9 (8/97) | "Return to the Forbidden Planet, Part 1 of 2" | Chris Cooper | Chris Renaud | Andy Lanning | Omega Squad is lead to Talos IV where they help Christopher Pike fight off the Jem'Hadar who have begun an invasion of Alpha Quadrant telepathic species. |
| #10 (9/97) | "Return to the Forbidden Planet, Part 2" | Chris Cooper | Chris Renaud | Andy Lanning | Omega Squad emerges victorious in fighting off the Jem'Hadar by destroying their stockpile of ketracel white, with the help of Talosians and their illusions. Pike had also been an illusion created to give the cadets courage and focus. Returning to Starfleet Academy, the squad learns it is to stand trial for having been on Talos IV. |
| #11 (10/97) | "Judgement" | Chris Cooper | John Royle | Tom Wegrzyn | Ambassador Spock offers to be legal counsel to Omega Squad and sways the judges by telling a story on how Jean-Luc Picard disobeyed the law to save the life of one of the judges. Omega Squad is nevertheless sentenced to death. |
| #12 (11/97) | "Renegades" | Chris Cooper | Chris Renaud | Andy Lanning | Omega Squad escape their jail cell and head for Deep Space Nine to find someone who will listen to their plea, and that the Dominion intends to invade all telepath worlds in the Alpha Quadrant. (The story is the first of 6 instalments spanning most of the Star Trek titles Marvel ran at the time. This is known as the Telepathy War, which continued in issues 12 and 13 of Star Trek: Deep Space Nine, issue 6 of Star Trek: Unlimited, issue 13 of Star Trek: Voyager (the least significant portion of the arc), and finally the special issue Star Trek: Telepathy War #1.) |
| #13 (12/97) | "Parent's Day" | Chris Cooper | John Royle | Tom Wegrzyn | It's parent's day at the Academy, and the cadets try to come to terms with their respective parents. |
| #14 (1/98) | "T'Priell Revealed, Part 1: Betrayal" | Chris Cooper | Chris Renaud | Andy Lanning | A sinister side of T'Priell, who appears Romulan, takes over her and makes her kidnap the rest of the squad with Zund. |
| #15 (2/98) | "T'Priell Revealed, Part 2: Origins" | Chris Cooper | Chris Renaud | Andy Lanning | The squad learns the truth about T'Priell. She died a few years prior, but not before having passed her katra to Selke, a Romulan she had befriended who looked remarkably like herself. With this, Selke was taken in by the Tal Shiar and brainwashed to believe she truly was T'Priell, so that she could infiltrate Starfleet Academy. |
| #16 (3/98) | "T'Priell Revealed, Part 3: The Fall" | Chris Cooper | Chris Renaud | Andy Lanning | The squad escapes with T'Priell/Selke. |
| #17 (4/98) | "Culture Clash" | Chris Cooper | John Royle | Tom Wegrzyn | Selke is taken to Vulcan to have T'Priell's katra removed, only to find that the minds are fused and must learn to cohabitate the same being. |
| #18 (5/98) | "mangHom qaD" or "Cadet Challenge" | Chris Cooper | Chris Renaud | Andy Lanning | This issue is told from the point of view of First Cadre (see issues 4 and 5) as they try to find the Sword of Kahless, which is only a ruse made up by Omega Squad to bring First Cadre to justice for the death of Kamilah. (This issue was published both in English and Klingon which made it at the time the first Star Trek comic book to be presented in this manner). |
| #19 (6/98) | "Between Love and Hate" | Chris Cooper | Chris Renaud | Andy Lanning | Pava faces her ex-lover, Kovold of First Cadre, only to learn that he and a teammate have been mutated by some unknown force. The series ends on a curious note, that this last story was told by Captain Edam Astrun several years in the future to one Fatimah, who could possibly be Kamilah's daughter. |
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