Molloy was elected to the Northern Ireland Forum in 1996 representing Mid Ulster and then for the same constituency to the Northern Ireland Assembly in 1998, 2003 and 2007. In 2005, Molloy was temporarily suspended from Sinn Féin after publicly disagreeing with the party policy on eliminating many district councils, including the Dungannon Council of which he was a member.[8]
In December 2012, he was selected as the Sinn Féin candidate for the UK parliamentary constituency of Mid Ulster, which had been held by his party colleague Martin McGuinness since the 1997 general election.[9] The Mid Ulster by-election took place on 7 March 2013, with Molloy winning with 46.9% of the vote.[10]
In the run-up to the by-election, media attention focussed on past allegations about Molloy and how they related to the DUP/UUP-supported independent candidate Nigel Lutton. In 2007, DUP MP David Simpson had claimed during a debate in the Westminster parliament that Molloy had been a member of the IRA and was suspected by police of being involved in the fatal shooting of Lutton's father, Frederick Lutton, on 1 May 1979. The IRA had taken responsibility for it on the basis he was an RUC reservist. The investigation came to nothing, and Simpson claimed this was because Molloy was subsequently coerced into becoming a police informant, providing information that helped break up the IRA's East Tyrone Brigade.[11] Molloy denied the allegations and challenged anyone to repeat them outside Parliament so he could take legal action (the original speech being subject to parliamentary privilege and thus not actionable).[citation needed] UUP leader Mike Nesbitt said he had been unaware of the speech and that it had played no part in Lutton's selection.[12] Lutton denied the claims were behind his decision to stand.[13]