The 2000s saw further changes both to laws and to structures of rugby in Ireland, with the provinces fully professional, most of our AIL winning team became full time players for the provinces and were no longer available to the club to any extent; and so a rebuilding began. Although the 2nd division was visited for a year (2004-05), the club progressed both on and off the field. Steven Hennessy and Peter Smyth developed a strong, mainly home produced squad, and took the club back to the top division the following season.
They continued to build, with many young promising players like Jonathan Sexton (now a star international player) and Mark Sexton, second generation Sweeneys, Robert (club international) and brother Richie (captain 2012-13), Conor Mc Inerney (both A Leinster and later Ospreys sadly retired due to injury), Paul Nash (Club Captain 2010-11), Conor Donohue, Kevin Sheahan, Ronan Doherty, Darragh Fanning (son of long time club, Leinster player and B international captain Declan), Phillip Brophy (Club Captain 2008-09 and club international), Barry O’Flanagan and Gavin Dunne, mingling well with our more mature players such as Gareth Logan (Club Captain 2007-08), Hugh Hogan (club International Captain and 2009-10) and Conor Mc Phillips (now coaching with Connacht). Younger players still, like Under 21 international and Leinster player Jack Mc Grath and U20 International Darren Hudson, Rob Hudson, Conor Hogan, Ray Crotty, Robbie Field, Ian O’Neill, Sean Preston and Joe Burns all were being integrated into the squad.
In 2008-09, the senior team ended the AIL 1st division season level with four other clubs, but due to points differential, controversially missed the play-offs (see reports), but the following season, 2009-10, playing under a new two-year experimental and highly competitive eight team division 1A, St Marys reached second in the league overall, made the play-offs, won the semi final and were narrowly beaten after extra time in the final (see reports). The season 2010-11, marked the end of the experimental AIL structure and was followed by a first division of two section, A and B, of ten teams each and second and third divisions of 16 teams each; all with relegation and promotion. Sadly, the club captain Paul Nash was injured during that season and had to retire from rugby, a great loss to the squad.