The build up and aftermath of the ship's arrival at 10am on March 3, 1961, was met with local nervousness and one of the "most active and sustained campaigns of protests in modern British history", according to Brian Lavery in an paper written for the British Maritime Museum.
Macmillan, who apparently agreed to the move during the meeting, was nevertheless cautious of the prospect and wrote in his diary: 'A picture could well be drawn of some frightful accident which might devastate the whole of Scotland.'
The Clyde was proposed as a potential site by the US. In return, the British could buy the American Skybolt air-launched missile to boost the RAF's V-bomber force, which had lost much of its credibility as a deterrent in the face of Soviet missile defences, according to Lavery.
Scotland was selected as a location for Polaris servicing given it would reduce the need for crews to head back to the United States after each 60-day patrol. Each journey home would take 10 to 14 days travel time which would cut into home leave.
In British naval headquarters, it was considered of prime importance for good political and military relationships that a base in US waters should be found.
The search for a base in Scotland was underway, under the code name Lamachus, with the Polaris service vessel to be based on a ship with shore facilities at an 'absolute minimum', Lavery said.
US Navy chiefs first favoured Gareloch as the location of choice, given its remote location and ease of access to Prestwick, the only transatlantic airport in Scotland at the time which was also popular given it was relatively fog free.
Macmillan favoured Loch Linnhe given the sparse population in the surrounding area, according to Lavery's account.
"From a security point of view, a robust population of three or four thousand Highlanders at Fort William is much more to my taste than the rather mixed population in the cosmopolitan city of Glasgow," he wrote.
Invergordon, Loch Ewe and Loch Linnhe were also proposed but rejected.
Four sites in the Firth of Clyde were also considered, including the channel between Largs and Cumbrae. Rothesay Bay, recently vacated by the British Third Submarine Flotilla which moved to Faslane on the Gareloch, was considered too high a safety risk.
As the operation to find a Scottish base gained momentum, so too did the activities of The Campaign for Nuclear Disarmament. Macmillan, Lavery said, showed signs of flapping in the face of rising public unease.
He had initially opposed Holy Loch and Gareloch given their close proximity to Glasgow and the likelihood for anti-nuclear demonstrations and the nervousness of ordinary people.
But after months of heavy negotiation, he announced that Holy Loch would be the site of the new base on November 1 1930 after the US Navy apparently convinced him of how difficult it would be to set off one of the Polaris missiles.
The site was relatively sheltered and easy to navigate. While a small population lived around the loch, it was felt they could be evacuated in the event of an emergency.
Macmillan was also of the understanding that "no decision to use these missiles will ever be taken without the fullest possible previous consultation". The Americans did not quite agree.
As the arrival date drew near, The Scottish Office wanted the ship to be berthed as quietly as possible but the Admirality wanted a far more high-profile approach to counter the profile of CND.
Lavery wrote: "Tension began to build up in the Holy Loch area in the days before the Proteus's arrival.
"The London Evening News of 2 March featured a local taxi driver looking over the loch and quoted him as saying 'I don't know whether to get rid of my taxi and buy an American car.'
"The local girls, it was said, waited in anticipation, the boys with apprehension. A lady who worked on Dunoon Pier spoke for many when she said 'I shall feel unsafe from the moment that ship comes into the loch'."
At 10am she was secured off a boy at Kilmun and dignitaries gathered. Naval officers appeared in full uniform, with swords and medals, and Provosts from surrounding towns appeared. Press arrived on board.
Later, a full social programme unfolded, with a reception in Queen's Hall, Dunoon, for 150 officers and enlisted men. The following night, a public dance was held.
Demonstrators wanted to build a barrier of canoes across the loch, but not enough manpower gathered and the passage of the ship was not halted. A small number of arrests were made.
On April 16, Proteus sailed to the North Channel between Scotland and Ireland for training. Small scale protests by canoeists were launched and one protester managed to hang on to the ship's bows but was forced to let go as the vessel picked up speed. Two demonstrators climbed up her side and one managed to stay in position for three hours.
Protests centred around the Holy Loch for months. In September, 400 demonstrators were stranded on a ferry due to bad weather. Others marched to US navy stores in Greenock
In London, 12,00 people demonstrated in Trafalgar Square against the Holy Loch base.
On November 1970, a fire erupted on USS Canopus at Holy Loch, killing three of those on board.
Four years later, the nuclear ballistic missile submarine USS James Madison collided with a Soviet submarine, during a dive just after departing from Holy Loch. A nine-foot scratch and a dent was left on her hull.
The base shut in June 1992 given the end of the Cold War and the arrival of new technologies.
Source: Brian Lavery (2001) The British government and the American Polaris base in the Clyde, Journal for Maritime Research, 3:1, 130-145.