The band replaced Mereschuk with Jay Randall and added former Cast Iron Hike guitarist Michael Gallagher before releasing the 1999 EP The Red Sea.

Bryant Clifford Meyer of The Gersch replaced Jay Randall in late 1999, and Isis remained with this lineup until their dissolution.

In 2002, Oceanic was released to critical acclaim,[2][3][4] and was the subject of a series of four vinyl reinterpretations by various contemporary artists; the series was consolidated into an Ipecac Recordings release, entitled Oceanic: Remixes & Reinterpretations.

[6] Panopticon was released in 2004, to further critical plaudits and an album of the year award from Rock Sound.

[11][12] "Holy Tears" and "Not in Rivers, but in Drops" were released from the album as singles in 2008, along with a limited-edition vinyl compilation box set entitled Shades of the Swarm later in the year.