[20][21] Following his return from suspension, Todd became a first team regular at Bolton Wanderers, forming a centre–back partnership with Guðni Bergsson, while also facing competition from Mark Fish.

[31] It wasn't until on 13 March 1999 when he made his return to first team, coming on as a late substitute, in a 2–1 win against Queens Park Rangers.

[33][34] He helped Bolton Wanderers reach the Football League First Division play-off final, as the club went on to lose 2–0 against Watford.

Just two days after being suspended by Bolton Wanderers, Todd then moved to Charlton Athletic, another Division One club, in "a £750,000 transfer, with 'add-ons' taking the deal to £1 million".

[52] Following this, he was initially welcomed back to the squad, playing for Charlton Athletic's reserve team before suffering an injury that kept him out for months.

[65] However in a match against his former club, Charlton Athletic, on 24 November 2022, Todd was at fault when he allowed the first two goals for the opposition team, as Blackburn Rovers went on to lose 3–1.

Ahead of 2003–04 season, Todd was put on the transfer list by manager Souness, due to lack of first-team opportunities under him.

[71] After being recalled by Souness due to Blackburn Rovers' defensive crisis, he made his first appearance of the season, starting the match, in a 1–0 loss against Charlton Athletic on 20 October 2003.

[72][73] Following his return, Todd was thrust straight back into Blackburn Rovers' first eleven with the team struggling near the bottom of the league.

[83] Even staying at the club when the summer transfer window closed and Mark Hughes appointed as a new manager, Todd remained out of the first team for three months, due to a knee injury.

[87] On 24 December 2004, in a buildup to a match against Newcastle United at the St James' Park, newspaper The Lancashire Telegraph mentioned Todd's name as he and Garry Flitcroft "are to be fired up for the visit of the under-fire".

[90] Todd was handed the Blackburn Rovers' captaincy by Mark Hughes following the departure of Barry Ferguson to Rangers, a recognition of his continued solid performances.

[96] During the near end of a 2005 FA Cup Semi Final against Arsenal, he elbowed Robin van Persie in the head, drawing blood, as Blackburn Rovers went on to lose 3–0.

[105] He then suffered a knock on two separate occasions during the match against Liverpool on 15 October 2005 and Charlton Athletic on 5 November 2005 but he made a full recovery.

[106] However, Todd received a straight red card in the 31st minute for handball, as the club went on to lose 2–0 against Everton on 3 December 2005, which saw him serve one match.

[110] After the match, manager Hughes acknowledged that he and Todd "have a difference of opinion over his decision to substitute him at Birmingham recently", but also revealed that the player suffered a knee injury that kept him out for the rest of the 2005–06 season.

[116] However, Todd was dropped from the squad by manager Hughes after he began to prefer using Nelsen and André Ooijer and told him to fight for his place in the first team.

Then Portsmouth manager Harry Redknapp was secretly filmed discussing the possibility of buying Todd with agent Peter Harrison, which is illegal under FA rules.

[120] Todd had, however, found first team opportunities hard to come by during the latter stages of the 2006–2007 season and went on to make thirteen appearances in all competitions.

After talks with Todd, Mark Hughes let it be known that he was available for transfer, leading to Derby County, Sunderland, Birmingham City, Wigan Athletic and Portsmouth all expressed an interest in signing him.

[125] Local newspaper The Lancashire Evening Telegraph reacted positively on his debut in the Clarets shirt, forming a centre–back partnership with David May.

Todd joined Derby County, a newly promoted Premier League club, for an undisclosed fee believed to be around £750,000 on 7 July 2007.

It was announced on 8 May 2008 that Todd was not in Jewell's plans for his restructuring of the Derby squad following relegation and he would be allowed to leave on a free transfer.

[137] His first game for Derby after returning from Northampton was the League Cup semi-final first leg against Manchester United, with Todd helping the club to a 1–0 victory.

On 22 April 2009, the Sydney Morning Herald reported that Todd signed for A-League club Perth Glory and would see out the rest of his career playing in Australia.

[149] On the last game of the season, Todd was named as captain for Perth Glory and kept a clean sheet, in a 2-0 win against Brisbane Roar.

[157] Todd made his return from injury, coming on as a second-half substitute, in a 0-0 draw against Gold Coast United on 3 January 2011.

On 27 January 2011, Todd joined Oldham Athletic after returning to the United Kingdom, signing a contract for the remainder of the season.

[164] On 14 October 2011, Todd moved to Hereford United, on a non-contract basis having previously been on trial with Port Vale and Burton Albion.

[169] On 26 April 2014, it was announced that Todd was appointed as the assistant manager to Warren Feeney at NIFL Premiership club Linfield in Northern Ireland, effective on 1 May 2014.