After six months of working in the class, Felder offered Kelly a job scripting Fantastic Four 2099 over a Karl Kesel plot.

At one point it was due to be canceled with #25, but a write-in and Internet campaign by fans led Marvel to reverse their decision.

Kelly's next major Marvel assignment was in late 1997, at the company's then bestselling title, X-Men, where he worked with penciller Carlos Pacheco.

After their run on that title finished the same creative team launched a twelve-issue limited series Justice League Elite featuring some of the characters from Action Comics #775.

Kelly has produced three creator-owned works: Steampunk, pencilled by Chris Bachalo and published by DC through Wildstorm's Cliffhanger imprint in 2000 (a second part, Drama Obscura, brought closure to the story, but Kelly has said he intends to eventually continue the book); M. Rex with penciller Duncan Rouleau, which was published by the now-defunct Avalon Studios (it was canceled after two issues); and Ballast, with penciller Ilya, a one-shot published by Active Images.

Kelly is a part of the Man of Action collective of creators (along with Joe Casey, Duncan Rouleau, Steven T. Seagle), who created the series Ben 10, currently airing on Cartoon Network.

He has published creator-owned work through Image Comics, including Four Eyes[6] and I Kill Giants,[7] as well as a graphic novel Douglas Fredericks and the House of They.