- Scenes were cut from the final game, possibly for timing. These scenes can be retrieved by completing the first disk on hard mode. The following scenes include:
- Shi Hao demanding his shipment of the Syphon Filter virus from an unknown caller.
- Archer's Blackhawk helicopter swooping low over Gabe on the train in Colorado.
- Teresa and Gabe in Moscow, trying to start up their shot-up van in Moscow. Gabe gets out to push.
- A bag lady in New York pushes a shopping cart across the street and a limo (presumably Mara Aramov's) runs it over, knocking down the bag lady.
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