It's 1942 and the crew of the S-33, a vintage WWI submarine is called back from shore leave. It seems that a German U-boat has been crippled in the North Atlantic and the U.S. Navy wants to intercept it and find her top-secret encryption device that has enabled German forces to communicate without American eavesdroppers deciphering their messages.
Commanding the S-33, which is now being retrofitted to look like another U-boat so that the crew can safely approach the mostly disabled German sub, is Lt. Commander Mike Dahlgren (BILL PAXTON) and his executive officer, Lt. Andrew Tyler (MATTHEW MCCONAUGHEY). He's not happy with the CO who's just thwarted Tyler's hopes of commanding his own vessel under the assumption that Tyler's not prepared to make the tough decisions such a commander must make.
Nonetheless, Tyler knows his duties and thus joins fellow officers Lt. Pete Emmett (JON BON JOVI) and Ensign Larson (MATTHEW SETTLE) in getting the enlisted men, including Chief Klough (HARVEY KEITEL), radioman Wentz (JACK NOSEWORTHY), the cook Eddie (T.C. CARSON), Trigger (THOMAS GUIRY), Mazzola (ERIK PALLADINO), Tank (DAVE POWER), Griggs (DERK CHEETWOOD) and Rabbit (WILL ESTES) on board and ready for action.
Despite Dahlgren being the CO, the mission is under the command of Lt. Hirsch (JAKE WEBER) and his assistant, Marine Major Coonan (David Keith). They brief the officers about the plan's mission of finding the U-boat, boarding her as disguised German sailors, taking prisoners and obtaining the encryption device.
Things, of course, go horribly wrong when the plan is enacted, with the S-33 being destroyed and most of the American and German sailors being killed. From that point on, Tyler, Klough and a small handful of the remaining crew take control of the partially disabled U-boat and must then contend with several perilous encounters with various German military vessels.