The club again made the play-off final in 1999, again at Wembley, this time defeating Leyton Orient 1–0 after a goal from Alex Calvo-Garcia. They were promoted to the Football League Division Two.

Their stay in this division was a short one and they were demoted again at the end of the following season.

They started the 2004/2005 season in Football League Two, but gained promotion to Football League One after a startling comeback season. The Club was nearly relegated to the Conference National the season before.

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In the 2004/5 season they led Chelsea, the Premiership champions, 1–0, in the FA Cup 3rd Round, but were denied as they eventually went down 3–1.