That's weird. As I remember it, you push the door open, make your way up past a few enemies, hit a T-junction, left takes you to a portcullis that doesn't open, right has a soldier sniping from behind a crate, go past him, up some stairs and you should reach a door to the roof. I've been through this a few times and it's always been straightforward.
Sadly, this may be a re-start-from-last-checkpoint job. That would sometimes happen in Painkiller but hasn't happened to me in NVN, yet.
Good luck.
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