Obadiah Stane, Howard Stark's old partner who runs the company, warns Tony that quitting weapons will ruin Stark Industries, and keeps asking about Tony's new work.
Stane is revealed to have been selling weapons to the Ten Rings and hiring them to kill Tony. He steals the reactor from Tony's chest to power his own armor.
The father figure who seemed to be protecting the company was the one who arranged Tony's capture. Both halves happen inside the first film.