During Brother, each of the band members’ children jumped into a bathtub placed at the side of the stage. Afterwards, Trey introduced them and wished everyone a happy Fathers’ Day. Funky Bitch was played in acknowledgement of a fan who had been holding up a sign requesting the song at this show and the previous one. Crosseyed and Painless included a brief, subtle tease from Page of the Grateful Dead’s Let It Grow. Trey teased Taste near the end of Disease, which was unfinished. Piper contained a brief Can’t You Hear Me Knocking tease. Frankenstein featured Page on the keytar and Trey on a five-neck guitar.

During Antelope, Trey changed the lyrics to “Been you to have any Hibachi?” The lyrics to Makisupa were changed to “Woke up this morning, pissing in jah cup / Woke up this afternoon, called my probation officer.” YEM contained a Gumsuckers March (Percy Grainger) tease from Page, was unfinished, and did not contain a bass and drums segment or a vocal jam.

After Limb By Limb, Trey introduced Fish as “Johnny B. Fishman” and quoted Johnny B. Goode, with Page also teasing "Charge!" before the quote. Split Open and Melt included a Can’t You Hear Me Knocking tease. Before the debut of The Connection, Mike introduced Trey as “Sweetie Pie” and Trey responded by blowing a kiss to Mike. There were severe thunderstorms during setbreak and, as a result, Page made an announcement that they were going to take a longer than usual break and that everyone on the lawn should return to their cars until the second set, which would not start until 11:00.

This show featured the first Walk Away since October 5, 2000 (80 shows). Disease was unfinished. After Grind, Trey remarked that Page blew the wrong note on the pitch pipe and had them all singing in the wrong key. They decided to perform another a cappella song and Trey joked that if they couldn’t get it right, Fish would sing Bike. Sure enough, Hello My Baby was no better and was aborted. However, true to his word, Trey announced that Fish will now sing Bike. For his part, Fish took the opportunity to welcome everyone to “the trainwreck portion of the show.” Bike was played for the first time since September 12, 2000 (95 shows).

Reba did not have the whistling ending. Trey and Fish teased Seven Below before Halley’s Comet.

This show, performed on the What Stage, closed out the 2009 Bonnaroo Festival. Before Mustang Sally, Trey remarked that he had seen a show at Jadwin Gym at Princeton University when was 12 (apparently referring to a 11/1/78 performance by Bruce Springsteen at this 3,000 seat venue, though Trey would have been 14 at the time), and added that Phish would now have an opportunity to play with one of his heroes, Bruce Springsteen. Springsteen joined in on guitar and vocals for Mustang Sally, Bobby Jean and Glory Days. Mustang Sally was played for the first time since August 5, 1988 (1,280 shows). This show marked the Phish debuts of Bobby Jean and Glory Days. Limb By Limb contained a Dave’s Energy Guide tease.

This show marked Phish’s first appearance at Bonnaroo. This “late-night set” on the What Stage began at approximately 11:00 p.m. Highway to Hell was played for the first time since February 26, 1997 (327 shows). YEM contained a brief Salt Peanuts (aka Basie Boogie) tease from Page.

This was the soundcheck for Phish’s Bonnaroo performances.

Reba did not have the whistling ending. Hello My Baby was played for the first time since December 5, 1999 (140 shows). Frankenstein featured Page on keytar.

This show featured the Phish debuts of When the Cactus is in Bloom and Alaska. Before Dog Faced Boy, Trey explained that while living with Fish, he wrote Dog Faced Boy, Tube and Gumbo based on entries in one of Fish’s journals. During Dog Faced Boy, Fish left his drum kit and lay down in front of the stage because he didn’t need to sing the song. Lengthwise (performed a cappella) was played for the first time since July 28, 1998 (235 shows). Bold as Love was played for the first time since October 6, 2000 (74 shows).

After forgetting the lyrics to Fee, Trey remarked that “We knew this one backstage.” This show marked the debuts of Sugar Shack and Joy. Before the extended encore, Trey asked, “You guys in a rush to go anywhere?” He then talked about how much they had enjoyed the northeast run and that they wanted to play a few more songs before heading south (though he was careful to note that they love the south, too).

Let Me Lie made its Phish debut at this show. The first post-break-up Makisupa Policeman notably did not contain a “keyword.”

During I Didn’t Know, Trey introduced Fish as “Little Junior Moses Brown Heaps DeWitt” and commented that he was going to “suck all of the moisture out of the air.” During Ya Mar, Page teased It’s Raining, It’s Pouring. Trey teased Flat Fee prior to Disease, which was unfinished. Twist featured an Oye Como Va jam. This show marked the debut of Twenty Years Later.

Drowned featured After Midnight and Jumpin’ Jack Flash teases. Meatstick was played in a different key than normal.

Stealing Time From the Faulty Plan and Kill Devil Falls both debuted at this show, with the latter, remarkably, being played by request. This show featured the first If I Could since June 28, 2000 (103 shows).

The Star Spangled Banner was performed from the pitcher's mound. This show marked the debut of Ocelot and the Phish debuts of Light and Time Turns Elastic. Stash was preceded by Stash, It's Ice and Take Me Out to the Ballgame teases. Trey also teased Take Me Out to the Ballgame after Stash and again during Limb By Limb. After Time Turns Elastic, Trey jokingly announced, "That's our single." The Ballad of Curtis Loew was performed for the first time since August 2, 1993 (628 shows).