Muldoon had an injury called patellar tendinitis in both his knees. In December 2004, he underwent surgery on one of his knees. The operation was successful and he resumed training on April 2005. Muldoon started the 2006 Ulster Championship campaign very brightly scoring 1–03 (6) in the first round of the Ulster Championship against defending All-Ireland Champions Tyrone and 0-04 against Donegal. However Muldoon, with a previously exemplary disciplinary record at all levels, was red-carded late in that game. Some commentators called for Muldoon's red card to be rescinded after television replays showed he was reacting to "extreme provocation" from Donegal full back Paddy Campbell, who had punched Muldoon in the groin. Muldoon however received a four-week suspension and missed Derry's next two games against Kildare and Longford. Longford produced a shock victory to knock Derry out of the 2006 Championship. He finished the 2006 campaign with 1-07 (10) from two matches.