I never got that from viewing it personally. Serpentor flew out the window even.
He flew out the window of the dome they were in or whatever but that dome was still under the mountain which imploded in a grand thermonuclear-esque explosion. I can't remember the name of the script writer for the movie but he does the commentary on the blu-ray and he basically said that his instructions from Hasbro were basically to "wipe the slate clean" on the bad guys in case they wanted to do a full villainous reboot.
He said the movie was supposedly to kill everyone off but in an ambiguous, off-screen kind of way so Hasbro could bring anyone back that they wanted.