That's a really cool idea with 990 in there! and HOLY CRAP! I just realized this guy -
http://tnypic.net/c49b1.png - is 990!
Anyways, I think the intro sequence would be best short, so how about something where you have the dream with 990 and then you wake up to the intro sequence? As for the actual dream, the SCP engine doesn't exactly render faces in very high detail, so I was thinking we have the player see 990 from behind on a bench or something (like the image on the Foundation's page - this also adds mystery as you don't know and can't see who exactly he is). Since he predicts future events, he could say something like:
990: The doors won't respond to any of our attempts to close it...
D-9341: What the hell?
990: If I were you, I wouldn't wake up my friend.
Later in the game the player could find a document on SCP-990 or on redacted incidents involving him, which would create a "mind=blown" moment for players who had no clue what happened in the beginning of the intro. Anyways, that's enough of my rant, I'm just throwing ideas (hopefully they aren't cheezy) around - but overall love the 990 idea! Since his image flashes around the start page, why not make him impact the game in some way
