McGrath resigned as chair of the technical group in October 2012, after a dispute with Mick Wallace, over Wallace's participation in the loose alliance related to speaking rights in the Dáil. He joined the Independent Alliance at its inception in 2016. He contested the 2016 general election under that banner, in Dublin Bay North owing to the abolition of Dublin North-Central. He was re-elected to the Dáil and then entered talks on government formation. On 6 May 2016, he entered Government with Fine Gael, under Taoiseach Enda Kenny, as Minister of State for Disability Issues. McGrath was also appointed a "Super Junior Minister", meaning he attends cabinet meetings but cannot vote.