I think this is the incident you're referring to, Santa:
http://en.wikipedia.org/wiki/Vasili_Arkhipov#Cuban_Missile_Crisis
More here: http://discuss.washingtonpost.com/zforum/02/sp_world_blanton101602.htm
"The most surprising new evidence revealed that we were even closer to nuclear war than the policymakers knew at the time, and that's saying something, because on Saturday, October 27, Robert McNamara thought he might not live to see the sunrise. At the time, there was a crescendo of bad news: a U-2 shot down over Cuba, another U-2 straying over Siberia with US Air Force jets (also armed with nuclear air-to-air missiles) scrambling to head off possible MIG interception. The Joint Chiefs had recommended air strike and invasion of Cuba, as of 4 p.m. The Cubans were firing on all the low-level US recon flights. At the conference, we found out that exactly at that moment, US destroyers were dropping signaling depth charges on a Soviet submarine near the quarantine line that was carrying a nuclear-tipped torpedo -- totally unbeknownst to the US Navy. The Soviet captain lost his temper, there could be a world war up there, let's take some of them down with us, etc. Cooler heads prevailed, specifically the sub brigade deputy commander named Vasily Arkhipov, who was onboard and calmed the captain down. The sub came to the surface about 15 minutes after Soviet ambassador Dobrynin left Bobby Kennedy's office carrying RFK's urgent message to Khrushchev, time is running out, invasion in 48 hours, if you take the missiles out, we will pledge not to invade Cuba, plus we'll take our missiles out of Turkey as long as you don't mention that part of it publicly. Early the next morning, Khrushchev announced the Soviet missiles would be coming out. "