For me, have the Suicide Squad accidently find a portal to the Marvel Universe. They start working on stealing advanced technology and kidnap some of Marvel's top scientists.(Moira McTaggart/Beast/Forge/etc (Xmen). Amanda Waller is the initial villain, but it flows into a Xmen/Suicide Squad/Black Widow/Checkmate issue. Especially if one or two scientist (Moira) decides to claim asylum.
It would be more of a spy thriller at first. It flows into the overall big-team fight later on.