First of all, Ben Reilly clearly died. Plus, if it's another Spider-Man clone, technically it wouldn't be Ben Reilly because Ben Reilly had certain experiences during his five year "exile" that made him who he is. There's a couple of possibilities for Ben Reilly's return:
1. Peter, since quiting the registration side is on the run, and since everyone knows Spider-Man is Peter Parker, Peter adopts the identity of "Ben Reilly" as an alias when he's not in costume.
2. Spider-Man is assumed to be dead. This forces Peter to not only adopt the "Ben Reilly" alias to ensure his enemies don't find out he's still alive, but decides to don the Black Costume, promoting the idea that, when Peter first wore it, people thought he was a different Spider-Man because he wasn't wearing the red and blues. Here, it promotes the idea in the publics mind that A. There were two different Spider-Men running around and that the black costumed Spidey had been missing in action for years until his "return" or B. That Peter Parker (who everyone thinks is dead) was not the real Spider-Man.
3. There is a "Ben Reilly", who is not only Peter's clone but was a clone created by Tony Stark. Just as Stark cloned Thor, he also cloned other Avengers as part of the fifty state initivite, including Spider-Man. However, the Spider-Man clone, like the Thor clone, was psychotic, but had somehow escaped (everyone assumed the clone disintegrated after it left its cloning chamber) and quickly realized the truth about what he was. So, in revenge, he decides to get rid of Spider-Man by sending the Vulture on him.