The four-issue Marvel Comics miniseries is set in an alternate reality where the superpowered mercenary sets out to destroy the publisher's most popular characters.
The title will see Deadpool kill the Avengers, followed by the X-Men and the Punisher.
"As soon as [editor Jordan D White] mentioned this project to me, I knew this would be my chance to present a version of Deadpool unlike anything fans have seen before," Bunn told Comic Book Resources.
"He's still Deadpool. He's still funny. But he's being seen through a dark, unsettling filter.
"His motivations aren't connected to many of the story elements you might have seen in other books," Bunn continued.
"This kind of tale gives us the chance to do some things we couldn't even think about in the core Deadpool book. But I wanted a catalyst for Deadpool's killing spree that could happen in the main book."
Bunn was recently announced as the new solo writer on Venom.
Deadpool Kills the Marvel Universe follows on from similar outings for the Punisher and Wolverine.
The series will run weekly through August, with art by Dalibor Talajic.