Back in the Southern League, the 1997-98 season saw mixed fortunes on the pitch – a promising start fading during the middle of the campaign to a sixth place finish – but major changes off the pitch. The independent supporters club took over the running of the club in December 1997 following an agreement with the major shareholder Corporate Equity, who had provided several cash injections to keep the club afloat. Steve Hall was installed as chairman and they celebrated this with a re-launch week in March, which included a new club badge and a series of events, a HTV-screened documentary by world famous film director, and new City director, Ken Loach the highlight. One of the new board’s first actions was to sack manager Steve Millard – in hospital at the time – and install former City star Paul Bodin as the new boss. The background to all these events was a familiar tale though, of £1000 a week losses and the search for a site for a new ground.

Bodin’s first season in charge got off to a winning start but a return to the Conference never looked likely – Nuneaton Borough running away with the league title – though an 8-0 win over Boston United was a highlight in their fourth place finish. The next season saw City lose just once in their opening 31 league matches and going into March they were battling Boston United for the title. However, injuries and suspensions were increasingly stretching their squad, and the final month of the season saw their hopes fall away, leaving the Lincolnshire side to claim the title, although subsequent revelations about financial irregularities at York Street showed that City were part of a very unfair battle. The season was still memorable for the brief cameo from future Premier League striker Bobby Zamora – on a month’s loan from Bristol Rovers - and a second successive 30-goal season for Martin Paul, so hopes of another successful season in 2000-01 were high. However, this turned out to be a false hope as City looked a pale shadow of the side from the previous year, spending most of the season in mid-table before falling away once again in the closing months to end up in 15th place.

Away from these disappointing events the club also suffered another blow in March 2001 when a shareholders vote over the possible sale of Twerton Park failed to reach the 75% majority required. Two potential deals were on the table – one involving a down payment of £100,000 – but the vote left City once again in limbo, with debts now reaching £425,000. In an attempt to regain greater control of the club the board announced an ambitious proposal to raise around £1/4 million to buy the 51% shareholding owned by Corporate Equity. The immediate effect of the ‘no’ vote was a budget cut for the 2001-02 season and a reduction in Bodin’s role to part-time. To the surprise of no-one within a couple of days of the season end the former Welsh international resigned and with him went a number of players, including Paul, Jon Holloway and Sal Bibbo. The man brought in to pick up the pieces was Alan Pridham, making the step up from Western League Paulton Rovers. With over 50 players pulling on a City shirt the next campaign it was a tough first year for Pridham, and for a long time relegation to the Southern League Southern Division looked likely before a memorable last day win at Worcester City secured their Premier Division place. The next season was much less eventful as City spent it around mid-table but in January 2003 the now-named Bath City Society reached its target of £235,000 to complete the buy-back of the club – the final £3000 donated by then Gloucester City chairman Colin Gardener following an appeal on BBC Points West.

The 2003 close season saw City hold celebrations to mark the 25th anniversary of their 1977-78 Southern League title win but it was a less ambitious target that faced Pridham and his players come August. Re-organisation of non-league football would see the introduction of a new two-league system between the Conference and Southern/Ryman/Unibond leagues from the 2004-05 season and a top 13 place finish was required to guarantee a place in this brave new world.