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Air Ministry authority dated 18 March 1958 was given for the closure of 3MU Milton during the second half of 1958 and therefore RAF Woodcote would be run down and closed by January 1959.

In the meantime Woodcote continued to issue equipment. On 3 June 1958 the last and final Annual Inspection was carried out by Air Vice Marshal E.N.Lowe, the Air Officer Commanding 40 Group, and in September the Air Officer Commanding Maintenance Command, Air Marshal H.D.Jackman paid a surprise and unofficial visit to the Unit. This visit coincided with the meeting of the Local Industrial Whitley Committee and he took the opportunity to talk to them on the subject of the closure of the site. On 29 January 1959 all personnel and stores remaining were transferred to 3MU Milton and the site closed down.

Air Ministry Minute No.172/59 confirmed the disbandment and reduction to inactive status with effect from 31 January.

Air Ministry Minute No.304/59 transferred the inactive site from Maintenance Command to Transport Command, under the responsibility of RAF Benson with effect from 29 May 1959.

By November Captain Goldsmith, who had been a leading campaigner with Henley RDC for the closure of RAF Woodcote, now had another battle on his hands, this time with Oxfordshire County Council who had refused him permission to retain, for agricultural uses, buildings No.5 and Nos 19A to 19G inclusive, on HQ Site, which were standing on his land. On appeal to an enquiry the Minister for Town and County Planning allowed these buildings to stand; the remains of which are barely visible today.

Other owners of land were not so lucky and where the RAF had not dismantled the buildings they were required to have them raised to the ground as the terms of the requisition required the RAF to return the land to the same condition as they found it. The Oxfordshire County Council had a strong view over this area of outstanding natural beauty and would do their best to enforce this arrangement. Owners who had no use for the buildings were more than content with this decision.

Jack Hatt, who in 1953 or 1954 bought from the Garton Estates at £28 per acre the part of Site 1 which had the Storage Sheds 9 -13 and the others buildings erected on them recalls that the site was already run down then. When the land was returned to him in 1960 all the Storage Sheds had been cut off at the base. The steel girders that formed the frame of the Sheds were not driven into the ground, but encased in the cement base. This made the erection of the sheds easier but also made the demolition easier, except that by cutting the frame at the base it left jagged pieces of steel sticking out of the ground which damaged his lorry tyres. Other sheds that could be removed, were and he believes that all the buildings that were removed were sold and sent to Egypt. Those that had no real value were demolished on site, or at least that was the plan. When the RAF had left Jack was still due to demolish the boiler house and the dope sheds, the search room and blast shelters and he has still yet to get around to doing this!

By April 1960 there was something different to complain about. The new nuisance was go karting on the concrete areas at Site No.1 between Storage Sheds 9 and 10/10a on the former Maintenance Unit site, but this time it was no longer the concern of the RAF.

On 28 August 1961 the Ministry of Defence flew its last survey flight over Woodcote and the three black and white photographs taken confirmed to them that all the storage sheds and other large buildings had been demolished. The bare concrete hard standings clearly stood out as white rectangles amongst the black woodland.

The Woodcote and Exlade Street by-pass was completed in 1970 when it cut through the open farmland between the two villages. It starts on the old B479 at Site 3 between Sheds 37 and 38 and goes north passing Exlade Street on the east and Woodcote on the west and is now known as the A4074. In subsequent years travelling Gypsies have illegally made camp on the concrete bases at Site 3 until evicted and more recently an illegal and unlicensed 'rave' was held during the hours of darkness, also on Site 3.