[4] In December 2005, midway through his second season as the Scarlets' starting openside flanker, Thomas signed a contract extension, keeping him with the region for another two or three years.
[5] At the end of the season, the Scarlets reached the final of the 2005–06 Powergen Cup; Thomas started the match, but was unable to prevent a 26–10 loss to London Wasps.
Thomas started each of the Scarlets' first eight matches in 2008–09; however, in an Anglo-Welsh Cup game against Northampton Saints in November 2008, after coming on as a substitute, he suffered a torn Achilles tendon that ruled him out for the remainder of the season.
He then played twice in warm-up matches ahead of the 2003 Rugby World Cup, coming on as a replacement in a 43–9 loss to England at the Millennium Stadium[29] before starting in a 54–8 win over Romania at the Racecourse Ground in Wrexham, scoring the fifth of Wales' six tries.
[30] After that, following his move to the Ospreys and subsequently to the Scarlets, Thomas was left out of the Wales team for over three years, returning for two tests against Argentina in June 2006, receiving a yellow card in the first for killing the ball.
For Wales' tour of Australia in the summer, coach Gareth Jenkins elected to leave out 18 of his key players in favour of sending them for intensive conditioning ahead of the 2007 Rugby World Cup, including back rowers Martyn Williams, Ryan Jones and Alix Popham;[35] despite fellow openside flankers Colin Charvis and Robin Sowden-Taylor also touring,[36] Thomas won the battle to become the first-choice openside and started in both tests.
[41] With Martyn Williams opting not to tour and Sam Warburton suffering an injury in the South Africa match, Thomas was left as the only specialist openside in the squad,[42] and was named in the Wales starting line-up for the first time in three years for the first test against New Zealand in Dunedin on 19 June 2010.
[43][44] He retained the starting openside position for the second test, but was sin-binned in the 70th minute for punching New Zealand lock Sam Whitelock in retaliation after he had been illegally held at a maul.