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A former Welsh international centre back, Dennis Wise signed Williams on a year's contract after he was released from Wise's previous club Coventry City in the summer of 2006. After admitting that Sean O'Hanlon would have kept the role had he not controversially left the club for MK Dons, Wise immediately installed Williams as his new club captain - though after a groin injury disrupted his pre-season campaign, Williams wasn't to make his debut until the third match of the season - a 1-0 victory over Rochdale.
The addition of Williams' experience and leadership qualities to the defence clearly benefitted the Town, particularly Jerel Ifil - Swindon's strong start to the season based on a sound defence, rather than flowing attacking football. It was a strange October for Williams though - firstly, after a serious arm injury to Peter Brezovan, Williams found himself between the sticks for the last ten minutes of a 3-0 victory over Grimsby, and then, at the end of the month, after Dennis Wise left the club to take over at Leeds, Williams took over the reins on a caretaker basis, and was given six games to prove himself as manager. Williams dropped himself for his second match in charge to concentrate on his managerial role, but despite this, the appointment of Barry Hunter as his assistant, and the signing of keeper Andy Lonergan, the Town lost both the matches he presided over. By the time the next match came, Paul Sturrock was appointed as manager, with Williams' caretaker position cut short, he commendably returned to his role of club captain, back in the heart of the defence.
Williams continued to lead the side up until early February, when he picked up a knee ligament injury after making a challenge in the final few minutes of a top-of-the-table clash against Hartlepool, a tackle for which he was booked. After the injury was originally described as just a "tweak", Williams was eventually forced to undergo an exploratory operation, which revealed more significant damage - and while the Town were very obviously missing his presence at the back, he underwent cruciate reconstruction surgery late in March that ruled him out for the season. Despite this, and the possibility that the injury could keep him out of the start of the following campaign, Williams signed a year's extension to his deal at the end of the season.
When Paul Sturrock resigned as manager in November 2007, Williams was once again to take over the Town hotseat - this time sharing the role with youth team manager Dave Byrne. A defensive injury crisis saw Williams named on the bench the following month - and with captain Hasney Aljofree lasting eighty minutes against Hartlepool, Williams took to the field, and promptly tore his hamstring, being substituted himself just four minutes later. Williams and Byrne helped to steady the ship after the departure of Sturrock, and when the club was taken over the following month with new manager Maurice Malpas taking charge, Williams took on a coaching position amidst speculation that he was to call time on his playing career.
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