Keenan would return to Tool as well as sponsoring solo work under the band name Puscifer. Howerdel would release a solo album, Keep Telling Myself It's Alright, under the name Ashes Divide.
During the down time, band activity was sporadic; the band reformed in 2010, and played live shows on and off between 2010 and 2013, but fell into inactivity after the release of their greatest hits album, Three Sixty (2013), and a live album box set, A Perfect Circle Live: Featuring Stone and Echo in late 2013. The band would formally reform in 2017 to record a fourth album, Eat the Elephant (2018).
Prone to downtime due to Keenan's other musical commitments, the band has featured a variety of musicians throughout alternating periods of activity and inactivity, and changed line-ups on each album, leaving Keenan and Howerdel as the only constant members. The original version of the band included Paz Lenchantin (bass), Troy Van Leeuwen (guitar) and Josh Freese (drums). Primus drummer Tim Alexander briefly stood in as a drummer prior to Freese in the band's initial live shows; prior to releasing any material. Band collaborator and producer Danny Lohner along with Marilyn Manson bassist Jeordie White were also members for a short period in the early 2000s. The band's latest lineup featured The Smashing Pumpkins guitarist James Iha, bassist Matt McJunkins, and drummer Jeff Friedl, the previous two also members of the aforementioned Puscifer and Ashes Divide projects.