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- Acid Rain TP - Skywarp and Hookshot insulted a mysterious fortune teller who was invading 'Con territory. Since they chased him off, guns blazing (well, Skywarp's guns, anyway), a mysterious acid rain has been falling on Polyhex- and the fortuneteller has been taking credit for it.
- Bad Nanos TP - A mech's damaged nanites have gone haywire, and are now trying to re-make everyone in his damaged mold.
- Crystal City Space Launch/Solar Construction CC Space Launch TP - Crystal City prepares for a space launch then builds a solar array on one of the moons.
- Cosmic Rust TP - A rusting disease caused by a fungus spreads across Cybertron; a cure must be found.
- CSI Iahex - Horizon dies under mysterious circumstances; Prowl tries to find out who dun it.
- Cubricron Itch TP - A case of Cubricron Itch spreads amongst the Cons and the Bots both.
- Deet TP - A mysterious alien ship wanders Cybertron, calling for her missing pilot- a being named Psyke.
- Depth TP - A otherworldly being from the future crash lands, let the insanity begin.
- Dragon TP - A otherworldly creature hunts and eats Cybertronians.
- Fumik TP - A very ancient mech awakens and begins the search to find items that will make him young again.
- Gangs Of Cubicron TP - Cubicron Don Vespa's organization is under threat of being taken over by his rival, Don Fiasco. Streetwise, Vespa's adopted son, is caught up in the mix.
- Gestalt Genesis TP - Individual mechs discover there is more to them as a group than meets the eye; stars the Protectobots.
- IBex TP - A huge herd of iBex are seriously causing issues. The Decepticons come up with a violent way to deal with them.* Seeker Shakeup TP - (Decepticon) The command trine of Starscream, Thundercracker, and Skywarp has been broken up as a punishment for Starscream, and he has been removed as air commander temporarily for disobeying orders.
- Nobyl TP - A ancient hero of legend awakens, but it is not a good thing that he has done so.
- Nucleon TP - The Decepticons discover Nucleon.
- Resounce Redeployment - The Autobots look for new resources by stopping the Cons from getting their own as well as try to make a new weapon to combat the Con aerial superiority.
- Roboraptors - Roboraptors run rampant!
- Search for Weldbond - Arcee seeks out her creator, Weldbond
- Shambleau TP - Otherworldly beings are discovered in the underground tunnels and end up infesting several Cons and Bots. A cure must be found to rid of them from the infected as well as chase them off the planet.
- Space Pirates TP - Arr mateys, here be pirates from space wanting yer booty!
- Sunday Bloody Sunday TP - Underground nonster truck rallies are ferreted out and stopped.
- Time Warp/Out of Universe (OOU) TP - The Decepticons create a time traveling machine and their first trip screws with the timeline temporarily.
- Tron Games TP - The Decepticons hold the Tron games for their warriors to show off their stuff.
- Trypticon TP - A 'city' is discovered by the Decepticons, slowly repaired, then activated. The Autobots must find a way to stop the beast.
- Vendetta TP - Don Vespa, a crimelord in Cubicron, has given Lifeline an ultimatum - stop associating with the Autobots, or else.
- Voyager TP - The Autobots retrieve a crashed sattellite of otherworldly origin and work to repair it to send it back from where it originated.
- War of the Roses - Starring Bankshot and Mirage.