Two pipers stood on the casing of the 8,400-tonne boat to greet the first Sea Lord, Admiral Sir Jock Slater, at the end of the historic final patrol.
Controversy has dogged the fleet of four Polaris boats since they took over the role of carrying Britain's nuclear deterrent from the RAF amid great secrecy in 1968. For 28 years they guaranteed Britain's national security with continuous patrols in the North Atlantic with their arsenal of 16 strategic nuclear missiles.
Despite the end of the Cold War, Russian submarines are still trying to track the Navy's ballistic-missile submarines. Now responsibility for Britain's nuclear deterrent will fall on two new Trident submarines.
The 16,000-ton Vanguard, which entered service in 1994 and Victorious, which entered service last September, are more advanced than Polaris and carry the more potent D-5 missile with a 5,000-mile range.
"There is a tremendous sense of occasion that after 28 years this is the very last time," said Commander David Phillips, 40, Repulse's Commanding Officer.
The demise of the Polaris fleet was sad for senior serviceman Philip Ullathorne, 47, from Selby, West Yorkshire, a veteran of 25 patrols. "It is the end of a hell of a good class of submarine which has done a fantastic job", he said.
The nuclear warheads will be unloaded and returned to the Atomic Weapons Establishment at Aldermaston, Berkshire, and the Polaris missiles will be broken up.
Repulse will be tied up and left to rust quietly at Rosyth, Fife, until a better solution for disposal can be found.
"It's like losing an old friend," said Admiral Whetstone. "Repulse has served everyone who has commanded her very well."Reuse content