In the level "Interval 09 - Incursion - Lapdog", there is a secret room that contains a whiteboard texture previously featured in an earlier game developed by Monolith Productions, Shogo: Mobile Armor Division, as well as a radio that plays audio of a news station reading traffic reports in Maritopa, a town from that game, before playing "Negai (Wish)", the game's theme song.

The character Jin Sun-Kwon was originally planned to be a sniper with enhanced hearing, but this was changed when Monolith Productions had trouble designing scenarios in which she could snipe. The influence of her original sniper role can still be seen in the elbow pads she wears and the red trigger fingers of both her gloves.

According to Craig Hubbard, the game's lead designer, a car chase sequence was originally planned to appear in the game. The sequence has even had extensive drafting carried out during development, but it was eventually removed because it didn't work out the way the creators hoped it would.

The car itself, however, made it into the game in a limited capacity; it is the same one that Spoiler:Rodney Betters drives the protagonist to the Birthing Facility in.

During early development of the game, there was a second villain named Conrad Krieg, but he was removed from the final release. His personality and outfit were merged with the game's main villain, Paxton Fettel.