He went on to make 36 appearances in 2003–04, with the club's regular keeper Mark Goodlad out injured. He played 32 games in the inaugural season of League One. He was limited to a single EFL Trophy appearance in 2005–06, as the club's No. 1 Goodlad enjoyed his first injury-free season since Brain's arrival.
Macclesfield Town
In June 2006 he was once more signed by Horton, who had since taken up the management position at Macclesfield Town.[7] After playing just nine league games for his new club, Brain suffered a broken leg on 25 November 2006, after colliding with Andrew Teague (who also broke his leg) in a game against Stockport County, and was ruled out for the rest of the season.[8][9]
Initially turning down a new contract,[2] he was given a short-term contract at the start of the 2007–08 season,[10] and went on to make a successful return from his injury to reclaim his place as Macclesfield's first-choice goalkeeper, making thirty appearances in all competitions. At the end of the season, managerKeith Alexander offered Brain a three-year contract, which he signed.[6]
In 2008–09 he played 52 games to become only the third player in the club's history to enjoy an ever-present campaign in the Football League.[2] At the end of the 2009–10 season he was named in the League Two Team of the Week for the last week of March,[11][12] but was released by the club after turning down a new contract.[13]
Walsall
He signed a one-year deal with Walsall in June 2010.[14] He started off the 2010–11 season as first-choice goalkeeper, before losing his place to club legend Jimmy Walker, who was re-signed in October 2010.[15] Brain vowed to win his first-team place back off the 37-year-old,[16] who was signed after a poor start to the season by Brain.[17] At the end of the campaign Brain as released, whilst Walker was offered a new deal.[18]