The pre-season saw Brian Horton sign Irish goalkeeper Dean Delany (Everton); midfielder Marc Bridge-Wilkinson (Derby County);[2] and Michael Twiss (Manchester United)[3] – all on free transfers.

[5] The season opened with a disappointing 4–1 defeat at Boundary Park to Oldham Athletic, though the Vale then recovered to record two 3–0 victories.

[7] Jamaican international striker Onandi Lowe also arrived on a short-team deal, and Wayne Gray joined on loan from Wimbledon.

In February, Vale then found their feet and managed to avoid defeat to Stoke at the Britannia Stadium, losing just three of their final 21 league games.

On 24 March, Liam Burns replaced an injured Mark Goodlad in goal 28 minutes into a home fixture with Wigan Athletic and a solid defensive performance helped the outfield player to retain a clean sheet.

A cup run and numerous fixture postponements meant the club were forced to play eight games in April, of which only two ended in defeat; for this achievement, Horton was named Manager of the Month.

Tony Naylor was the club's top-scorer with 21 goals in all competitions, with new players Bridge-Wilkinson and Brooker also hitting double figures.

"[19] Machin handed Brian Horton a 60-section questionnaire on each player on the team every two weeks and was branded as "belligerent, uncooperative and bizarre" by the League Managers Association.

In October, Machin tells the press that he would sack Brian Horton if the club had the money to pay for his severance package; meanwhile, Marketing Manager Rob Edwards resigned after less than two months into the job.

Dave Jolley (who had previously resigned at Stockport County after proposing a move to Maine Road[20]) was appointed Chief Executive in February.

[24] Vale responded to the humiliation by putting five players on the transfer list: Liam Burns, Ville Viljanen, Sagi Burton, Jeff Minton and Michael Twiss.

It was a two-legged affair with Lincoln City, and Vale were the victors with a 2–0 win at Sincil Bank, thanks to goals from Bridge-Wilkinson and Naylor.

[29] Vale lifted the trophy for the second time with a 2–1 victory, Bridge-Wilkinson and Steve Brooker scoring the goals on a rainy day in front of 25,654 spectators at the Millennium Stadium; Brooker scored the game's opening goal from the penalty spot after Naylor was fouled by Darren Powell on 77 minutes.