The series was published by Aircel Comics, an imprint of Malibu Comics, which was eventually bought out by Marvel Comics, which went on to publish three of its own one-shot Men in Black comic books (they were based on the live-action films, rather than the original comics, however; the company did bring creator Lowell Cunningham back to write them and also reprinted the very first issue of MiB, though).
- Continuity Nod: The one-shot Far Cry published by Marvel was made to retell the story mixing both the comics and the first movie. Here, Agent Jay is the one seen in the comics and his "recruitment" was made in the same way (even he was undercover for the new drug Bezerk), but the technology is more like the one seen in the first movie.
- Cult Defector: The first mission of Agent Jay revolved around a new kind of drug, the Bezerk, and a cult that developed around around it. Jay has the mission of going undercover in this cult, being used by K as a Guinea Pig, rescuing Jay before he died and annihilating all the cult.
- Evil Is Not a Toy: One of the stories was about a group of kids playing a Dungeons & Dragons clone, who found an ancient mystical artifact and used it as their 20-sider. (They didn't know it was magic, they just thought it was cool-looking.) When one of them casts a "summon demon" spell, an actual demon appeared and destroyed half their house, and most of the town they lived in.
- Exactly What It Says on the Tin: The drug in the first issue is called "Bezerk," and being in contact with it becomes the user into The Berserker.
- The Faceless: Agent Zed, he has his first appearance physically in the movies, in the comics he was just a voice.
- Fantasy Kitchen Sink: Unlike its film and animated adaptations, the Men in Black also monitors mutants, demons, and other paranormal creatures and activities.
- HeelFace Turn: Agent Ecks.
- Jerkass: Kay, which might surprise people who are only familiar with the films, making the acting of Tommy Lee Jones as a smoothing of the version seen in the comics.
- Knight Templar
- Short-Runners: The original run was two volumes of three issues each volume. When The Movie came out, three more MIB comics were made - one a straight retelling of the film, one taking place between movies 1 and 2, and only one a continuation of Lowell Cunningham's original miniseries (Far Cry, more as The Remake).
- The Men in Black: Duh.
- The Nameless: Justified in the Men in Black, but the future Agent Jay has no official name in his first appearance before being "recruited".
- The New Rock & Roll: Seemingly parodied in the third issue, in which a game of a faux-D&D actually causes a demon to breach our reality.
- The Remake: The Far Cry one-issue comic book, made by one of the original creators, Lowell Cunningham, and the only color comic based on the original series than the movies.
- Unexpectedly Real Magic: One of the stories was about a group of kids playing a Dungeons And Dragons clone who found an ancient mystical artifact and used it as their 20-sider. They didn't know it was magic, they just thought it was cool-looking. When one of them casts a "summon demon" spell, an actual demon appeared and destroyed half their house, and most of the town they lived in.
- Villain Protagonist: Kay all over. He neuralizes an entire street with abandon, leaves Jay to deal with a grieving mother and, in a later issue, brainwashes a neuralized hick into climbing a clock tower with a rifle, then committing suicide, on his 16th birthday. Why? "For insurance." All for the greater good, of course.
- Well-Intentioned Extremist: Kay. He genuinely believes that keeping the paranormal secret is for the "greater good".
- White Sheep: Jay. He mantains his own principles even after being recruited as a MIB (or at least he tries to).