At the start of Ya Mar, a naked guy jumped onstage and ran around for a bit before being rounded up by security, prompting Trey to observe that "Naked Guy's" antics "took a lot of balls." During Ya Mar, Mike changed the lyrics to "he was a naked pa." Trey sang the verses to Light out of order. The sound for Mike's bass dropped out during Golgi leading Trey to label it the "trio version." During the ensuing Antelope, Mike took a bass solo to make up for the bass everyone missed in Golgi. Antelope also contained several lyric changes referencing the naked stage crasher.

Reba did not have the whistling ending and Scents did not have the intro.

Disease was unfinished.

Peaches was played for the first time since September 24, 1999 (188 shows). The lyrics to Antelope were changed to "Been you to have any Mike, man?".

Nellie Kane was played for the first time since July 1, 2000 (137 shows). Before Meat, Trey announced (in a reference to Meat's lyrics) that Mike had changed his name and is now "The Artist Formerly Known as Cactus" and "The Artist Presently Known as Prince."  Subsequently, during Meat, Trey introduced Mike as "Prince" and Fish as "Prince's alter ego on the drums, 'Princess.'" Free Bird was played for the first time since June 22, 2000 (144 shows) and was performed a cappella for the first time since December 29, 1998 (223 shows).

This show featured the first Uncle Pen since July 11, 2000 (129 shows). Ghost contained a tease of Seven Below.

This show marked the Phish debut of Golden Age (TV on the Radio) and the debut of Tomorrow's Song. During Page's solo in Coil, the rest of the band left the stage.  Upon returning, Trey said that they had left for the encore and asked Page where he had been, leading into I Been Around. The Fire encore continued the tradition of Phish playing a Hendrix cover on the guitarist's birthday (11/27/92 and 11/27/96 being the other occasions).

Kill Devil Falls contained San-Ho-Zay teases from Trey. During Wilson, Trey implored Mike to take a "heavy metal bass solo" (and Mike complied). The lyrics to Antelope were changed to "Been you to have any Mike, man?" followed by another bass solo from Mike.

Cities was played in response to a fan with a sign requesting the song and featured alternative lyrics referencing Thanksgiving. Reba did not have the whistling ending. Disease was unfinished. Much of Weekapaug was played at a significantly slower pace than normal. Prior to ADITL, Fish teased the Weekapaug drumbeat.

BBFCFM included several references to Syracuse native Jon Fishman (including shout-outs to his alma mater, his father and his father's dental patients).

Albuquerque was played for the first time since September 14, 2000 (115 shows). Fish teased Buffalo Bill prior to Rock and Roll.

Disease was unfinished.