When you’re talking about a music festival whose inaugural event was literally wiped out by a typhoon, it can feel a bit petty to complain about the weather. All the same, campers arriving at Fuji Rock Festival in Naeba on Thursday last week might have hoped for a warmer welcome than the torrential downpour that greeted them. Though things improved as the weekend went on, the rain still managed to put a dampener on the proceedings, and might explain the muted reception afforded to some of the festival’s biggest acts.

This was no truer than for Roxy Music, whose headlining slot on Saturday was a soggy affair in every sense. The group were an awkward fit from the start, and their high-end lounge band schtick, informed more by the slick pop of final album “Avalon” than their art-rock roots, did little to engage a scattered and bedraggled crowd. After an interminable string of torch songs and soprano saxophone solos, they finally wheeled out the hits — “Virginia Plain,” “Love is the Drug,” “Do the Strand,” et al. — but few people had stuck around to hear them.

John Fogerty seemed equally out of place on the bill: The former Creedence Clearwater Revival mainstay was playing in Japan for the first time in 38 years, which was a good decade or so before most of the people at the festival were even born. But as he hurtled through a set that crammed more than 20 Southern rock classics into just over an hour, it quickly became clear that this was going to be one of the highlights of the weekend. As the final chords of “Proud Mary” rang out, a few thousand new converts fired off text messages home to admit that not all of the music in their parents’ record collections was rubbish.

This was the first edition of Fuji Rock where revelers didn’t have to contend with dreadful cell-phone reception, thanks to a series of booster antennas installed around the site. Twitter use was rife, and the micro-blogging site teemed with condensed reviews and news of celebrity sightings, along with links to set lists provided by the more web-savvy record labels. It’s tempting to speculate about how this will change the dynamic of the event in years to come; for one thing, the days when musicians could wander the site incognito are probably over.

Back in the real world, it was an unusually good year for indie hipsters. Vampire Weekend pulled off an assured midafternoon set on the Green Stage that marked them out as possible future headliners, even if singer Ezra Koenig’s carefully enunciated banter between songs made him sound like an eikaiwa (English language school) teacher. Foals might also make it to the big league: Their new album, “Total Life Forever,” has armed them with the kind of sweeping guitar anthems that main stages are made for, and singer Yannis Philippakis’ speaker-scaling antics suggested that he was up to the task.

Elsewhere on the bigger stages, you could witness a curious phenomenon: the moonlighting megastar. Members of Led Zeppelin, Radiohead, Red Hot Chili Peppers, Foo Fighters and Rage Against the Machine appeared over the three days, though none of them were with their regular bands.

By far the most eagerly anticipated among them was Atoms for Peace, a supergroup featuring Thom Yorke and Chili Peppers bassist Flea alongside producer Nigel Godrich and drummers Joey Waroniker and Mauro Refosco. It felt like the whole festival had turned up to catch a glimpse of the diminutive Radiohead frontman, who, with his headband and gray vest, looked like he’d been getting fashion tips from Keith Richards. He bopped and shadow-boxed around the stage as the band played percussive versions of tracks from his 2007 solo album, “The Eraser” — hardly the most crowd-pleasing body of work to draw on — before returning to play a few of the songs that people had actually wanted to hear.

A supergroup of a rather different kind, Them Crooked Vultures combined the talents of Led Zeppelin bassist John Paul Jones, Foo Fighters’ Dave Grohl and Queens of the Stone Age’s Josh Homme for an epic and somewhat over-indulgent jam session. “Scumbag Blues” was so distended, it felt like it might not wrap up in time for Summer Sonic the following weekend. The remainder of their set was seldom less than impressive, though also strangely forgettable — great pedigree, shame about the songs.

Zack de la Rocha, the polemic vocalist for Rage Against the Machine, scored a huge turnout for his appearance with current outfit One Day as a Lion, though it soon became apparent that the crowd was really just there to hear some of his old hits. They didn’t get them, and the end of the performance was greeted with what could best be described as mild bewilderment. There were similar reactions when arch contrarians MGMT took to the stage afterward and kicked off with an ocarina solo, but otherwise the band largely played to their strengths — including hit single “Kids” — rather than the self-sabotaging antics that have marked some of their recent shows.

Friday night headliners Muse were perhaps the safest bet on the bill, and their set delivered everything you’d expect: eye-popping visuals, industrial quantities of prog-rock excess and a drummer dressed like David Bowie in “The Man Who Fell to Earth.” For pure spectacle it took some beating, though the band feel increasingly at risk of descending into hollow bombast, and the lazy blues-rock jams tacked onto the end of songs suggested that they weren’t really operating at full throttle.

“Full throttle” didn’t even seem to be an option for Massive Attack. Much as it was nice to see founder member Grant “Daddy G” Marshall back in the fold, the trip-hop collective made for lousy company on a rainy Sunday evening. As they trudged from one drab, downtempo number to the next, it wasn’t so much moody as rather boring. It was left to Scissor Sisters, playing in the postheadliner “special guest” slot, to wrap things up properly. Even the increasingly foul weather and persistent technical problems couldn’t dull the luster of their energetically camp disco-pop, which is like catnip for festivalgoers.

One of the most pleasant surprises of the weekend came from Belle and Sebastian, the Scottish indie darlings who have morphed from fey popsters into a tremendously entertaining live band. Stuart Murdoch’s attempts to engage the crowd with stilted Japanese drew coos of “Kawaii,” and when he invited four of the audience onstage and paired them up to dance along to “The Boy with the Arab Strap,” it was a moment of quite spine-tingling sweetness.

Further down the bill, Dirty Projectors were on dazzling form, juggling complex rhythms and polyphonic vocals with ludicrous ease, while the festival gave Japanese audiences their first taste of Los Angeles’ Local Natives and New York’s

Yeasayer, both of whom rose to the occasion. British trio The xx had a live act that turned out to be less enthralling than their superb debut album: Songs drifted out of time, and the consistently downbeat tone made it feel like the slow dance at an indie disco stuck on repeat. When they were followed by Broken Social Scene, the difference was pronounced. The Canadian indie collective couldn’t quite reach the heights of their exuberant performance at Fuji Rock in 2006, but it was still heady stuff, their four-guitar lineup summoning a vast wave of emotions.

In a perverse bit of scheduling, LCD Soundsystem were on at the exact same time as Hot Chip, the band with whom they probably share the most fans, and they lost yet more of their audience as people rushed off to catch Atoms for Peace toward the end of their set. Those who stuck around were rewarded with one of the most ass-shaking shows of the festival, and it’s hard not to warm to Murphy’s persona: the podgy middle-aged music geek who somehow hit the big time.

Of course, with an event as sprawling as Fuji, half of the pleasure lies in making new discoveries. This year’s wild card was the Narasirato Pan Pipers, an ensemble from the Solomon Islands who popped up on a variety of different stages, as well as descending on the Stone Circle area to school people in the finer arts of tribal dancing. At the opposite end of the musical spectrum, beat-boxing wunderkind Beardyman dazzled with his ability to conjure dance-floor bangers using nothing but a few Kaoss Pad effectors and his own larynx. Genuine weirdness was a little harder to come by, although Japanese underground veterans Hikashu deserve special mention for supplying the best (and perhaps only) avant-garde jaw harp solo of the weekend.

Finally, there was the true hero of the event. Last year, the recently deceased Kiyoshiro Imawano was paid tribute with a star-studded performance on the Green Stage, featuring R&B legend Booker T. Jones and many others. This year, the task fell to a lone troubadour who stood by the main gate, playing songs by the flamboyant Japanese rocker on a battered acoustic guitar. It was smaller scale, sure, but it had heart.

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