The fallout from 2004 saw the period from 2005 to June 2008 become another time of uncertainty for Yes. It was part of the longest period of inactivity in the long history of the band and Jon Anderson's health continued to be a concern.

In the meantime, the members of the classic Yes lineup pursued various solo activities. Notably these included Chris Squire joining the reunion of The Syn and recording a new solo album. Alan White toured with The Syn, formed his own band White and recorded with Circa. Steve Howe joined the reunion of the original Asia lineup and formed the Steve Howe Trio. Rick Wakeman restricted his solo appearances to short tours and special shows while diversifying into TV and radio. Jon Anderson worked on numerous studio projects but limited his live appearances to short stints including brief tours with Rick Wakeman and the Paul Green School Of Rock All-Stars.

This period saw the release of three Yes live DVDs in "Songs From Tsongas" (recorded 2004, released in 2005), "Live at Montreux 2003" (released 2007) and "The New Director's Cut" version of "Yesspeak" (recorded 2003, released 2008). All three DVDs featured the classic Yes lineup and were very well made, with "Songs From Tsongas" making No.1 in the UK charts. Also released was "The Word Is Live" 3CD set in 2005, an extensive official bootleg collection of live performances recorded between 1970 and 1988.

In 2007 Yes appointed a new manager in Trudy Green of HK Management. Then in March 2008 Jon Anderson delighted fans by announcing that he would be doing an extensive world tour with Yes to celebrate the 40th anniversary of the band. Rick Wakeman declined for health reasons to undertake such a lengthy tour and instead nominated his eldest son 37-year-old Oliver as the replacement keyboard player. Tickets went on sale for the American leg of the tour that was to take place in July/August 2008. However, tragedy struck prior to the tour when Jon Anderson suffered acute respiratory failure and all dates had to be cancelled.