Hovis and Thibeaux split after Cotton Is King. Williams began to double on bass and Dana Mizer joined as the new drummer. The trio recorded its second album, 1998's Kontiki, on borrowed equipment in Harrison's garage, before handing the tapes over to producer Brad Jones to remix and add instruments to. The resulting album, a mélange of lo-fi production tropes and classic pop hooks, was rapturously received in the American pop underground, although its limited distribution kept it from breaking through in any meaningful way. Add the fact that Mizer left the group before the album was even released (although he does appear in the group photo on the sleeve) and it seemed like Cotton Mather were destined to fade into obscurity.

And they might have done just that, except for a fortuitous set of circumstances. Oasis guitarist and songwriter Noel Gallagher somehow got his hands on a copy of Kontiki, and in a rare moment of clarity, realized that what Cotton Mather was doing was a far superior and much more original version of what Oasis themselves had been attempting for years. Gallagher began talking up the American band to the British press, with the eventual result that the British psych-pop label Rainbow Quartz reissued Kontiki in the U.K. in late 1998. It was a massive indie hit, with the brilliant "My Before and After" even gaining a fair amount of radio airplay. Harrison and Williams quickly redrafted Mizer into the band and added new bassist Josh Gravelin for a successful U.K. tour, after which the foursome recorded 1999's EP Hotel Baltimore.

The revived group began recording a third full-length, with Jones again producing, in early 2001. The resulting album, The Big Picture, was released by Rainbow Quartz in late 2001. Parting ways in 2003, the bandmembers formed new groups. Most notable among them was Harrison's Future Clouds & Radar, which released two well-received albums in the late part of the decade. Cotton Mather's legacy proved strong, however, and in 2012 -- thanks to fan support solicited through a Kickstarter campaign -- Harrison released a deluxe double-disc reissue of Kontiki on his own Star Apple Kingdom label.