As more Masterpiece Theatre tracks found their way into DJ's hands, The Roots began performing these songs as well. But somewhere in the process, Black Thought's solo material evolved into what would become the most experimental Roots album to date. Phrenology, which was released in November 2002, would contain several Masterpiece tracks, including “Thought @ Work”, “Pussy Galore” and “Water”, although most were reworked by The Legendary. Most notable of the bunch was “Thought @ Work”, which originally featured a rare Beatles sample and fell victim to sample clearance issues. Luckily The Roots still perform a rendition of the song in its original form to this day.

Phrenology was almost an antithesis to Things Fall Apart, with Ben Kenney's guitar-work making for a more intricate and heavy sound, which translated to a deeper sounding live show. The lush instrumentation additions allowed The Roots' live sound to breach other genres of music, while still maintaining to keep hip hop at the forefront. “The Pros (The Roots is Takin' Over)",  “Rock You" or "Thought @ Work" typically started shows.  With new member Frank “Knuckles” Walker handling congas, bongos and drumpads alongside ?uestlove's rhythmic drum grooves, the band now featured a more intricate and hard-hitting percussion sound. “Thought @ Work” featured covers of “Apache” and “It's Just Begun” as an extended outro, and showcased the diversity of the additional percussion. “You Got Me” was now performed in an extended dub reggae jam, often with a cover of Outkast's “So Fresh and So Clean” thrown in for good measure. ?uestlove's drum solo was also greatly enhanced, as he now dueled in call-and-response fashion with Knuckles.

Other Phrenology tracks entering the fold included the single “Quills”, “Break You Off”, “Sacrifice", "Pussy Galore" and the hidden bonus cut "Rhymes and Ammo".

Through much of 2002 and 2003, The Roots toured with special guest Cody ChesnuTT. Together, they'd perform their smash hit “The Seed 2.0”. During this time, The Roots further experienced a shift in membership as well as their sound. Ben Kenney parted with The Roots to join Incubus in March 2003, leaving Vernon Reid of Living Colour fame to fill in on lead guitar for several months. Human turntablist Scratch left the band in June 2003, leaving The Legendary without a beatbox presence for the first time in almost a decade. It was also around this time that Martin Luther hit the road with The Roots to add his soulful vocals and guitar into the mix.

Although the roster adjustments couldn't have come at a worse time, it had little affect on their flourishing live show. Burnt Sugar's string assassin, “Captain” Kirk Douglas, joined the crew in the summer of 2003, adding his amazing Hendrix-meets-Santana style guitar work to the fold on a more permanent basis. As The Roots embarked on their Okayplayer Winter Tour in 2003 with their newly solidified band, they began premiering songs like “Web”, “Boom” and “I Don't Care”, leading the way for The Tipping Point.