The 1999-2000 season was Tranmere Rovers's finest ever in cup competition, with a run to the last eights of the FA Cup, and the final of the League Cup, the club's first major cup final. The League Cup final resulted in a 1-2 defeat against Leicester City, Rovers's goal scored by David Kelly after Rovers defender Clint Hill had foolishly got himself sent off; although it should also be added that the player he fouled had been clearly offside at the time. Remarkably, Aldridge took Rovers to the final of a major national cup competition with a team which did not include a single player he had paid a fee for. The club's severe financial constraints meant that at the time the squad included only a single player for whom a transfer fee had been paid, big striker Wayne Allison, who was cup-tied for the League Cup run.

The following season they again reached the FA Cup last eight with a run that included 2 matches unlikely ever to be forgotten. The fourth round witnessed Rovers drawn away to Merseyside rivals Everton, in whose shadow, along with that of Liverpool, the club has always lived. A memorably one-sided game, refereed by Jeff Winter saw Rovers give the Toffees a comprehensive three-nil hammering at Goodison Park, with one goal scpred by Jason Koumas and two storming headers from defender Steve Yates. The match has been immortalised in Rovers history, fans having dedicated 27 January Saint Yates' Day. More drama was to come in the shape of a 4-3 fifth round win over Southampton. Trailing 3-0 at half time, and having been comprehensively outplayed by the Premier League outfit, Rovers came out for the second half transformed. With Prenton Park a cauldron of noise, Rovers started to launch an astonishing display of unfettered positive football, ripping the Southampton defence to shreads as they blazed forward at will. A hat trick by Paul Rideout brought the scores level, Stuart Barlow then hitting the winner which gave Rovers a 4-3 victory in a game generally regarded as the greatest FA Cup comeback of all time.

In the league things were very different, with the side floundering at the very bottom of the table. Aldridge finally resigned in March 2001 when Rovers suffered a 2-3 defeat at home to Barnsley after having led 2-0. The caretaker team of Ray Mathias and Kevin Sheedy was unable to save them and Rovers were relegated from Division One after 10 years at that level.