After constant touring in 1998, the band started the new year by heading out on the Black Sabbath tour until mid-March. They then took some time of to record their new album. After relentless work in the studio, on October 26th 1999 Incubus released "Make Yourself" which included 13 tracks, and a guest appearance.
Right after the release of "Make Yourself", the band went on tour with Primus and Buckethead which lasted for the remainder of 1999. The band also put out the single, "Pardon Me" which began to play all over radio stations across the country. Soon, MTV picked up the video as Buzzworthy and Spankin New Music. To start off 2000, the band headed out on the Sno-Core Tour with System Of a Down, and Mr.Bungle until March, at which time they hit the road with label mates of Epic, Ultraspank until April.
Due to the success of Pardon Me, and the new acoustic version of the song that had such a huge buzz around it, Make Yourself hit Gold Status (500,000 copies) in April of 2000. The band then hit the road again, this time overseas, playing shows with Queen Adreena. They returned home at the end of May to go back on a tour of the United States with long time friends 311.
The second single released from "Make Yourself" was "Stellar", and the video received afternoon airplay on MTV, on TRL, and became a huge success on Billboards Modern Rock Chart. In July Incubus once again went out on the road with Ozzfest. Eventually realizing that the fans were loving the acoustic versions of songs from "Make Yourself" the band released a 6 song EP titled "When Incubus Attacks Volume 1" on August 22nd, 2000. In its first week, "When Incubus Attacks Volume 1" sold nearly 40,000 copies, and scored #41 on the Billboard Album Charts.
The band then took a short break after finishing the Ozzfest 2000 Tour, playing two acoustic shows at Artist Direct Studios. On October 05th, 2000, Make Yourself went Platinum (1,000,000), and shortly after, the band went on tour with Deftones and Taproot. Due to the growing number of fans searching for the impossible to find independent album, "Fungus Amongus", on November 7th, 2000, the band re-released the album with the same artwork and track listing as before. Also, the "Strait Up" record, a tribute to the late Lynn Strait of the band Snot, was released, and Brandon contributed his vocals to the song 'Divided', and Brandon and Mike appear in the video for another song off the record, 'Angels Son'. To finish off the year 2000, Incubus played back-to-back dates at the KROQ Almost Acoustic X-Mas. They performed with a full orchestra, and acoustic instruments, during the second night Brandon stated: "I think we took this acoustic Christmas a little too serious."
To start off 2001 the band released the third single off "Make Yourself", 'Drive' on January 15th. Shortly after, 'Drive' took off, moving quickly up to the top of the Modern Rock Charts eventually hitting the #1 spot. The band took a break for a while during the first part of 2001, before returning to a studio in Malibu, California to record the follow up album to "Make Yourself". They finally hit the road with Hundred Reasons in Europe from June until the first week of July. At this time the band were invited to play with the Area One Festival which featured: Moby, Nelly Furtado, and others. Also, in July "Make Yourself" went Double Platinum (selling 2 million copies). In August, the band got to play their first shows in Australia and Japan, before returning to the 'States' to begin their long awaited headlining tour with long-time friends from California, Hoobastank (formally Hoobustank). Meanwhile, the bands video for "Drive" was nominated for an MTV Video Music Award in the category Best Group Video. But in September of 2001, they lost that award to the pop group N’Sync.