The epilogue to Marvel Comics' summer event will mark the end of his run on the franchise.
"AvX is a complete story told over 12 issues and you get closure, but because it's the Marvel Universe there's always a lot of other stuff you want to explore," Gillen told Comic Book Resources.
"However, you don't want to do it in the new #1 issues of Marvel NOW! because that makes them anti-climatic and too reliant on what went before, which is the opposite of what a #1 should accomplish. Marvel asked me if I fancied doing that.
"I thought about it a bit and decided it was a chance to do some interesting character work. Plus, while it's not an epilogue to my Uncanny X-Men run, it was an interesting chance to say goodbye to those characters in a more leisurely format than usual, as opposed to with the Extinction Team shouting at each other on a battlefield."
Gillen revealed that he had planned to "dovetail" his run on Uncanny X-Men with the Avengers Vs. X-Men story.
"The status quo at the end of AvX leaves things interesting and leaves some characters particularly interesting," he continued. "Exploring that gives me more than enough space for a meaningful narrative."
The recently relaunched Uncanny X-Men will be one of nine titles cancelled in October to make way for the Marvel NOW! initiative.
A teaser has hinted that Gillen and Greg Land will be working on a new Invincible Iron Man series.