Slipper resigned from the Liberal National Party to become an independent speaker in the Westminster tradition upon taking office, pre-empting moves to expel him.

Ashby dropped his sexual harassment lawsuit in June 2014 with his case having been earlier dismissed as an abuse of process by Justice Steven Rares of the Federal Court of Australia.

[6] In 2010 Slipper drew significant local and national media attention over the alleged overuse of his parliamentary travel entitlements.

[15] On 14 August 2010, just as the travel abuse allegations were gaining momentum, it was revealed in the Sunshine Coast Daily that a move had been made to attempt to disendorse Slipper in favour of former MP Mal Brough for his seat of Fisher at the next election.

However, this move was rejected due to an agreement between the Liberal and National parties about guaranteed endorsement for existing candidates.

With this in mind, Labor believed that Slipper was a potential "weak link" in the Coalition, and sought to use him to bolster its parliamentary standing.

[5] On 28 September 2010, Slipper accepted Labor's nomination to serve as Deputy Speaker of the House of Representatives and was elected to that position by 78 votes to 71, defeating the Coalition nominee, Bruce Scott of the National Party.

[26] In November 2011, Harry Jenkins, a member of the Australian Labor Party, unexpectedly resigned as 26th Speaker of the House of Representatives.

Slipper resigned from the Liberal National Party on taking the Speaker's seat and continued in parliament as an independent representative.

[33] He also moved to reinstate once weekly the longer and more formal Speaker's procession into the House involving the Serjeant-at-Arms and the Mace, which had not been seen in three decades.

Ashby, a 33-year-old gay man,[38] alleged that Slipper sexually harassed him on a number of occasions, via mobile phone text messages and in private conversations.

A sexual harassment case regarding these allegations was dismissed by the Federal Court on 12 December 2012, after Slipper argued that the charges were "vexatious and an abuse of the legal process".

[43] The Coalition, as well as Rob Oakeshott, Andrew Wilkie and Tony Windsor,[44] called on Slipper to continue to stand aside pending a resolution of the sexual harassment claims.

[49] Federal Court Justice Steven Rares dismissed the sexual harassment charges against Slipper in December 2012, saying that he had "reached the firm conclusion that Mr Ashby's predominant purpose for bringing these proceedings was to pursue a political attack against Mr Slipper and not to vindicate any legal claim he may have for which the right to bring proceedings exists.

According to documents released by the court, Slipper was alleged to have used Cabcharge to pay for hire cars to visit a number of wineries in the Canberra region in January, April, and June 2010.

Justice John Burns reserved his decision until 26 February 2015, when he ruled the appeal be upheld and the conviction and sentence be set aside.

[58] However, key independent members Tony Windsor and Rob Oakeshott, despite voting against the earlier no confidence motion, later informed Slipper that they could not continue to support him as Speaker given the damning text messages.

[59][60] Slipper later entered Parliament and, when announcing his resignation, said:[61] I leave this position without rancour, with a great deal of sadness and, more importantly, with a great deal of regret because I believe that, given the controversy which has occurred in recent times, that it is in the interests of the Parliament that I should take the course of action that I have personally chosen to take.He then moved to the crossbench as an independent member of the House.

Brough subsequently faced a Federal Police investigation in relation his role concerning the theft of the Speaker's diary and announced he would not contest the following election.

In 2016, Slipper travelled to Brazil to be ordained as a deacon and priest and was instrumental in the CTS applying to join the Brazilian Catholic Apostolic Church (ICAB) in a unanimous vote of its synod in that year.