If I remember correctly Malgus merged the Foundry with the Space station of the Emperor(which he stole) and when you go up against him in the False Emperor you are actually fighting him on this new combined Foundry Space Station. Before you actually engage him, he orders the whole thing to self destruct. So If I remember correctly the Foundry is destroyed along with Malgus' empire.
Which was a VERY dumb decision, in my opinion.
"Well, you see all those flashpoints you did leading up to this? Screw those, here's an anti-climactic ending where we kill of a character that was so hyped up, so well-written and so loved by many that we just had to kill him off."
Such a wasted opportunity for expansion in that particular storyline. I really hope they bring it back sometime in the future.