G.I. Joe vs. the Transformers continuity
G.I. Joe vs. the Transformers is an ongoing series-of-miniseries published by Devil's Due, who holds the G.I. Joe comic-book license.
The JOEvTF universe is set apart from either the ongoing G.I. Joe or Transformers comics because of its overriding sense of fun. Because neither group of fans takes this crossover universe very seriously, it revels in its ability to do whatever it wants, kill important characters, or change the world. For example the fourth series seems to be a gleeful exercise in throwing as many ideas that fans love to hate as possible into one story (principally Cobra-La and the Pretenders) and telling a pulp adventure with them.
Production
Devil's Dues' G.I. Joe vs. the Transformers was originally the counterpart to Dreamwave's The Transformers vs. G.I. Joe. The series were published offset, so that the Dreamwave series began as the Devil's Due series ended, with little overlap in-between.
Devil's Due to change of the second series from 6 issues into 4 (with double-sized first and last issues) in order to get the last issue published before Dreamwave lost the Transformers license (and avoid the legal headache aroudn their right to publish the end of the series.)
Initially each series was not planned ahead of time, leading to a somewhat disjointed overall story arc (technology given to humans after the first story is being decommissioned at the beginning of the second.) Many different story ideas were considered for the second and third series, but subsequent series have followed 'seeds' (obvious hooks) of stories planted earlier.
A fifth series (if produced) is expected to feature Iron Klaw.
Universe
In 2004, the newly-founded Cobra unearthed the Ark, containing 39 Transformers, which it sought to reprogram to use as weapons, triggering a series of increasingly bizarre encounters between Earth and Cybertron.
Ironically this reboot of the G.I. Joe timeline, founding the organization in 2004 instead of 1982, makes most of the team children of the 80's.
The JOEvTF universe includes a version of the Beast Wars series in its past.
