As early as December 2008, Keenan had mentioned that he and Howerdel had passively and separately been writing new material for A Perfect Circle, although the band would officially remain in hiatus and largely out of the view of the public through mid-2010. The turning point was an unexpected collaboration between Keenan and Howerdel; Keenan was scheduled to perform a rendition of "Bohemian Rhapsody" with Queen guitarist Brian May in June at E3 2010, but May had to cancel at the last minute. In need of a guitarist, and knowing Howerdel was in the area, Keenan reached out, and had Howerdel play guitar for the performance at the last minute. Despite little time to prepare, the performance was a success, and afterwards, both felt more compelled to perform together again.
In September, the band officially announced the end of their hiatus, indicating they would again return to live performances. Keenan, Howerdel, Freese, and Iha all returned to their respective roles, though, with Lenchantin and White unavailable, the band recruited Matt McJunkins, touring bassist for Ashes Divide and Puscifer, to join as bassist. The performances, running through the end of 2010, included traveling to five separate cities for three nights of shows in each city, with each night containing a complete, in-order performance of one of each of their three albums – Mer de Noms, Thirteenth Step, and Emotive – notably being the first time most of the material from the latter had ever been performed live. Throughout the year the band would discuss the prospect of new material, but with uncertainty. Keenan continued to insist that logistics and industry trends made recording another full album unlikely, and that single one-off songs would be more likely. Howerdel noted that he had been writing material and presenting rough demos to Keenan since 2008, but that much of the material was in a state of flux, some being accepted by Keenan as potential A Perfect Circle material, while other being rejected by Keenan, and/or saved by Howerdel for a prospective Ashes Divide release in the future.
The band continued their live performances into 2011, including a North American tour that spanned May through August. Notable events included Rock on the Range, Edgefest, Ottawa Bluesfest, Kanrocksas Music Festival, Lollapalooza, a performance at the Red Rocks Amphitheatre. Freese, who had already committed to drumming for Weezer during the same time-frame, was only able to perform at the opening show, and was replaced by Jeff Friedl for the remainder of the shows, who, like McJunkins, had previously worked with both Ashes Divide and Puscifer. Keenan and Howerdel continued to allude to recording new music, but continued to state that the process was slow, the logistics of money and availability made it difficult, and that a full album was still unlikely, in favor of single songs instead. Only one new song, "By and Down", was performed at the shows. By the end of the year, Keenan revealed that none of the material was ready for release, and that moving into 2012, he and Howerdel were moving back into their respective other projects – Puscifer and Ashes Divide. The band was inactive over the course of 2012, outside of a single live show in December. However, just prior to the show, in October 2012, Freese announced he would be permanently leaving the band, with Friedl becoming his permanent replacement.
The band played a few live shows in early 2013, including Soundwave Music Festival in Australia and Lollapalooza Chile, though Keenan reported that they had still yet to complete any new tracks due to their other commitments. Later in the year, the band announced two separate compilation releases for November 2013. The first, a greatest hits album entitled Three Sixty, containing one new studio recording, "By and Down", and the second, a box set entitled A Perfect Circle Live: Featuring Stone and Echo. The box set contained four CDs of live music: one for each of their three entire-album performances of Mer de Noms, Thirteenth Step, and Emotive done in 2010, collectively dubbed Trifecta, and a recording of their 2011 performance at the Red Rocks Amphitheatre, dubbed Stone and Echo. The set also came with DVD video recording of the 2011 Stone and Echo performance. In promoting the releases, Howerdel commented on future releases once again, stating that he felt they had "75% of the foundation of [the next] A Perfect Circle record ready", though he conceded that they were still without Keenan's lyrics or vocal melodies, and could still change depending on Keenan's reaction to the material. He also conceded that they still disagreed on the release medium; Keenan preferred smaller releases, while Howerdel preferred the format of a full album. Shortly after, the band again fell into a few years of public inactivity, with little occurring outside of Howerdel's 2015 commentary reiterating his commitment to the band, and Keenan's early 2016 commentary reiterating he still hoped to return to the band.
