Following the completion of the tour, the band became absorbed in various side projects. Corgan did some music for the film Ransom. Iha and D'Arcy set up their own record label, Scratchie Records, distributed through Mercury. In 1997, Smashing Pumpkins recorded two songs for the soundtrack of the film, Batman and Robin. After this there was little action. Corgan obliquely referred to another Smashing Pumpkins album, but time passed without any appearing. James Iha released a solo album in 1998 called Let It Come Down, feuling speculation that the band was about to break up.

They didn't however, and finally delivered an album, Adore, in July 1998. Adore is a peculiar album on the surface until it has been carefully digested; then it makes perfect sense. The first thing that strikes the listener is its quiet, elegiac sound. Nearly gone are the supertextured guitars and Brian May style crunchers. Instead, it sounds like a continuation of the melancholy strains of "1979" and the artistic grandiosity of "Tonight Tonight". This came as a disappointment to many fans, who mourned the loss of the band's hard edge. However, it is not a bad album. Lacking Chamberlin, drum machines and guest drummers handle the beat, which gave Corgan an opportunity (or reason) to change the band's sound, bringing in synthesizers reminiscent of the Cure, and dubbing them over beds of acoustic guitars. In the end, it's a dream-pop art record; not what the fans wanted, perhaps, but perhaps what they should have expected. The long wait for the album helped it reach #2 on the charts, but it didn't show the staying power of previous releases, and failed to yield any hits.

The band kept a fairly low profile again in 1999; they busied themselves recording a follow-up. Jimmy Chamberlin returned to the band, which excited fans hoping for a return to hard rock. The new album appeared in 2000, with the bizarre title, MACHINA/The Machines of God.

The title is a giveaway; Corgan finally made good on what had always seemed likely to happen someday; he made a progressive rock album in the true 70's sense, with a vague, muddled plot, song fragments that fade into each other, with moments of bombast and head-scratching conceits. Unlike in the past, Corgan didn't mask his arty ambitions with a subversive veneer of hard rock, or lush layers of melancholy. Instead, he wears his ambition on his sleeve, which didn't result in the most becoming of albums. Chamberlin's return does indeed boost the hard rock factor; "The Everlasting Gaze" and "Heavy Metal Machine" have guts to them, but they're rendered almost impotent by the density of production. There is little sense of band cohesion again; most of the record sounds like Corgan's obsessive lone overdubbing again. D'Arcy left the band just prior to the album's release; it peaked at #4 but faded fast, once again yielding no hits.

Corgan then announced his intentions to end Smashing Pumpkins after a farewell tour. Hole bassist Melissa Auf Der Maur was enlisted to fill D'Arcy's spot. For the faithful, Corgan performed the unselfish gesture of releasing 25 tracks left over from the MACHINA sessions as Machina II: The Friends and Enemies of Modern Music free for download over the internet. Interestingly, MACHINA II is much superior to MACHINA, featuring some of the classic hard rock fans had thirsted for, as well as one of the most unlikely James Brown covers ever, "Soul Power". There are full band workouts, and Corgan studio constructions, plus a variety of appealing experiments. Not everything works, but the price was right, and it was the thought that counted. Bringing their career full circle, the band played its final show on December 2, 2000 at Cabaret Metro in Chicago, site of their first gig.

Corgan assembled a new band in 2001, Zwan, with Chamberlin, plus guitarist David Pajo (ex-Slint, ex-Tortoise), guitarist Matt Sweeney (ex-Chavez), and bassist Paz Lenchantin (ex-A Perfect Circle). Their debut, Mary Star Of The Sea, came out in January 2003 to generally positive reviews. If anything, this is the long-awaited real followup to Siamese Dream; it features Corgan's trademark layered guitars, and a solid, hard rock aesthetic, with shades of art rock. What is startling about the record is Corgan's demeanor; for the first time ever, he actually sounds like he's in a good mood. It also represents one of the best guitar albums of the early 00's, an unusually dry period for guitar albums. The album peaked at #3, and was a promising debut on all levels, but Corgan announced in September 2003 that he was breaking up the band.