The Transformers Universe comic series was released through the Official Transformers Collector's Club. It came to an end when the liscense for the club and convention was given to Master Collector.
Transformers: Universe #1
On the reformatted techno-organic Cybertron Cheetor, Rattrap, Silverbolt and Blackarachnia were interviewed by the Autobot reporter Rook. They then welcomed the Autobots Roulette, Shadowstriker, Sideswipe, Sunstreaker and Trailbreaker back to Cybertron. Buzzsaw, Quickstrike and Rockbuster were also present. The returning Autobots along with Blackarachnia and Silverbolt were then abducted via teleportation beams and taken to Unicron. Tap-Out, Transformers: Armada Megatron, Brawn, War Within Grimlock and Snarl were also abducted from various timelines. Silverbolt, Blackarachnia, Sideswipe and Sunstreaker were forcibly reformatted by Unicron. Taken captive by Razorclaw, Reptilion, Obsidian, Tankor and Striker, the Autobots were forced to fight one another. They witnessed Armada Smokescreen kill Generation One Smokescreen, whose spark was absorbed by Unicron. Sensing the need for a champion Primus and Alpha Trion brought Optimus Primal back to life.
Transformers: Universe #2
After the events of the Botcon 2003 voice actor play, Optimus Primal is able to use his spark telepathy to free Striker from Unicron's influence. Sideswipe and Sunstreaker are forced to fight. Optimus Primal helps break free the slaves from various timelines which are held there and gets them to Cybertron. Blackarachnia and Shadow Striker defect to the Decepticons and stay behind. Blackarachnia discovers Tarantulas is working for Unicron.
Transformers: Universe #3
Optimus Primal pleads with Magnaboss and the Maximal council (which includes Bantor, Airhammer, Choroda, Torca and Battle Unicorn) to take the threat of Unicron seriously, but they doubt his claims. Optimus Primal is detained, but Snarl frees him. Alpha Trion and Primus claim they need Primal to choose his troops for any Cybertonians past of present, and he chooses Rhinox and Depth Charge, who are brought back to life. Although Rhinox is happy to have a second chance to redeem himself, Depth Charge isn't pleased with being brought back from the dead. Depth Charge rescues Rattrap from an attack by Blackarachnia.
Transformers: Universe - Wreckers #1
Starts with a flashback to late Generation One, where Daniel Witwicky and Wheelie are killed. This Daniel's friend Arcee into a sad state. Hot Rod and Springer talk about becoming Maximals. Main story is set in the later episodes of Beast Machines. In "Departure" the Wreckers, Mutants and Dinobots arrive on Cybertron and are sent on missions by the Oracle. Arcee, Dillo, Mol, Rav, Skywarp, Cyclonus, Rotorbolt and Devcon join the Wreckers. Contained Primeval Dawn Part 1, a story set on the Beast Wars Earth just after the Maximals left at the end of the Beast Wars televison series. The Vok return Airazor and Tigatron to Earth as Transmetals, and then use the Matrix from Optimus Prime, the Transmetal 2 Driver and the control suit from the Beast Wars which was used by Quickstrike to control Optimal Optimus to create Primal Prime. We learn Tarantulas (Fox Kids repaint colors) and Ravage (Transmetal 2 Tripredacus Agent version) are still alive and are making a new army of Predacons.
Transformers: Universe - Wreckers #2
In "Betrayal" - the Dinobots are attacked by the Dweller. Mutants are killed by the Quintessons. The Wreckers meet Glyph and Tap-Out. Cyclonus betrays the Wreckers for his true master, Cryotek. Contained Primeval Dawn Part 2. The Maximals are joined by Ramulus. The Predacons (Ravage, Razorclaw, Spittor and Iguanus) attack as Tarantulas rips the Matrix out of Primal Prime.
Transformers: Universe - Wreckers #3
The Wreckers rescue a banished Quintesson who tells them a story of the origin of Cybertron. Dinobots meet up with Devcon, who is hunting Cryotek. Contained Primeval Dawn Part 3. Primal Prime is reanimated by the Vok.
Transformers: Universe - Wreckers #4
Unreleased issue. Main story would have merged the story with the other Universe comic. Artwork released on the internet contained appearances of the Dinobots, Reptron, Devcon, Rook, Snarl, Skydive, Longhorn, Che and the Monsterbots. Story involved the invasion of Cybertron by the Quintessons. Would have contained Primeval Dawn Part 4, the last part of that story. Presumably the story would have contained the death of Airazor, the defeat of Tarantulas and the Maximals being joined by Fractyl, Packrat, Spittor and Sonar and returning to Cybertron.