Lt. Hiram Coffey (Michael Biehn) carries a 9x19mm SIG-Sauer P226 as his sidearm. At the time of the movie, the SIG 226 was replacing the Beretta M9 as the standard-issue sidearm in the U.S. Navy SEAL teams. TRIVIA: In the screenplay, this weapon was described as a ".45", presumably a 1911 variant.
When he suspects a threat to the nuclear warhead, Navy SEAL Lt. Hiram Coffey (Michael Biehn) takes out a MAC-10 with a detachable barrel extension and gives it to Fellow SEAL Schoenick (Christopher Murphy). TRIVIA: In the screenplay, this weapon was a "CAR-15 short-barreled assault rifle."
M16A2 assault rifles are carried by the armed Navy personnel on board the Benthyic Explorer. At least one of the M16A2s seen in the movie appears to have a "slab side" lower receiver unit, which means that it may be either a civilian AR-15 A2 semi-automatic rifle being used as a stand-in for an M16A2, or simply an A2 upper on a full-auto M16 (SP1) lower.
In the Special Edition, two Soviet sailors were seen with AK-47s slung over their shoulders when the massive tsunami approached a Soviet naval base. It can be also seen in the war footage the aliens present to Bud when he encounters the aliens.
