Critters scamper through A Ghost Is Born, the extraordinary finale of Jeff Tweedy and Wilco’s most experimental era. Birds, bees, bugs, dogs, and spiders poke their heads out of lyrics steeped in celestial abstraction, cry out over seiches of art rock, and retreat to the shadows. Years later, in his memoir, Tweedy would explain how the animals arrived during the album’s writing phase, a time when he was getting walloped by multiple chronic disorders, subsequent opioid addiction, and mistreatment at the hands of negligent medical professionals—the combination of which would soon culminate in weeks of in-patient rehab. “I was pretty sure I was going to die,” he wrote. “It felt like a big flood was coming, something no one could survive. So I was saving anything I could, piling it all onto this ark.” These animals—each representing a different aspect of his personality, so that his family might be able to posthumously piece him together—served a higher purpose: Jeff Tweedy was writing his own epitaph, his swan song.

He would survive the deluge, but the idea—Wilco’s Noah’s Ark concept album—would not: He ditched that blueprint midway through. And ultimately, A Ghost Is Born is more dynamic and ambitious than a biblical flood metaphor rock album probably could have been. Wilco’s fifth LP is at various points head-splittingly noisy, hypnotically hushed, a bloodletting, a blast, and it all amounts to a wider exploration of what it means to care amid a surrounding world’s collapse. Twenty-plus years after its initial release—and commemorated here with a gargantuan 13-piece box set that exhaustively pieces together its rocky origins—it has never sounded so enduring.

By 2003, Wilco were reaching levels so high that their chemistry and capabilities as a full band simply needed to shine above all. Early that year, Tweedy made an adventurous debut album with Loose Fur, his avant-garde side project with drummer and percussionist Glenn Kotche and composer and studio utility knife Jim O’Rourke, whose auspicious introduction three years earlier made sparks fly and later reinjected Wilco with newfound creative abandon (and politicking) after Tweedy brought them into the fold. O’Rourke’s inside-out touch behind the boards would become the new standard after his mixing offered the final, code-cracking breakthrough to Yankee Hotel Foxtrot, a eulogic dissection of man and nation through a kaleidoscopic Americana lens that happened to coincide with the September 11 attacks and was soon followed by the invasion of Iraq.

O’Rourke played a major role in A Ghost Is Born from start to finish, this time as co-producer and occasional supporting player. By now intimately familiar with the respective personalities of the senior band members, including bassist John Stirratt and multi-instrumentalist Leroy Bach, he brings out their best, especially on “Muzzle of Bees.” O’Rourke wrote the delicately fingerpicked opening, which the band gradually assembles into a sophisticated apex while Tweedy seems to exhale words of naturalistic impressionism. By the time it reaches its stunning instrumental coda, its fine contours are swarming with overdriven amp fuzz. O’Rourke—in that era a full-time member of Sonic Youth who had already had a hand in over 200 albums, including some indie classics—was floored by the final mix. He realized just how badly Tweedy was struggling when he watched him react to the same mix with indifference.

Kotche, meanwhile, was also around from the jump for the first time, and his percussion-first mind guides him into A Ghost Is Born’s alternatingly beating and murmuring heart. “I think that the drum kit hasn’t been explored enough outside of the parameters of groove-based jazz or rock,” he said in The Wilco Book that same year. “I also like to view the drummer’s limbs as a quartet, with each appendage having its own role and responsibility.” Kotche makes good on both statements throughout Ghost, where he is an absolute menace of mysterious texture intersecting with crisp, nuanced backbeats. “Company in My Back” is among his classic performances: a relaxed 2/4 groove that seems to grow antennae when his hammered dulcimer launches the chorus into the skies and a sound imitating a clicking beetle creeps across a suddenly quieter middle verse.

That sound is one of many “inglenntions,” as Tweedy dubbed them, that are all over A Ghost Is Born. Kotche had an ingenious way with quotidian, makeshift instruments, including sculptures, hubcaps, and electric fans; at least two descriptive captions in his sketchbook—“chambers of chains” and “pressure devices”—even became lyrics on the whisper-soft meditation “Wishful Thinking,” which Kotche lightly scratches up with some metallic, bustling background noise. The song’s stop-you-in-your-tracks outro gently repeats one solitary question about its title over and over, like chest compressions on a stuffed animal: What would we be without it? It’s a sneakily stirring reflection on optimism as a means of survival, a philosophy that Tweedy spoke about with the rock critic Greg Kot for his 2004 band biography Learning How to Die, released one week before Ghost. “A lot of times I write things as wishful thinking, or as reminders, because I can invent a person that can believe that to sing it,” he said. “And in doing that, I feel I’m taking some proactive step to being that person.”

A few such plainspoken exceptions aside, Tweedy’s lyrics are as surreal as ever here. In Adult Head, his 2004 book of poems that were adapted into lyrics for the album (he once called his own poetry “raw material to cannibalize for my songs”), animalia-dissolved apparitions spill off the page; “he thinks maybe the world is some kind of kitten,” wrote Sonic Youth’s Thurston Moore on the back cover. The animals remaining from the ark idea, untethered by their original symbolism, become personified hallucinations that stalk A Ghost Is Born: They laugh, they sing, they fill out tax returns on a private beach. Elsewhere, Tweedy selected pairings of words from random, categorized columns that elicited unexpected emotional responses, like the numbers on computer screens in the TV series Severance. He drew inspiration from the children’s books he would read to his kids, which were often written from animal perspectives and which prompted him to narrate “Company in my Back” as a bug at a picnic, as well as books by Henry Miller, whose Stand Still Like the Hummingbird informed “Hummingbird,” a lovely tune about living on through memory that’s about as plain-English as the album gets.

“Hummingbird” was almost a humming, drone-based track, but was reborn as a bouncing piano-pop delight thanks to Mikael Jorgensen, who began the A Ghost Is Born sessions as an assistant at Tortoise’s Soma Studios in Chicago and ended up a full-time Wilco member for the next two decades and counting. Living and working among the “silly Wicker Park Mafia” (as he puts it in Bob Mehr’s thorough liner-notes essay, partially adapted from his 2004 band profile for the Chicago Reader) of audiophiles and record junkies from which Liz Phair once famously sang about exiling, Jorgensen found his own way out by becoming Ghost’s surprise final puzzle piece. His dual expertise as a gifted pianist and studio engineer filled two of the many skill-set voids left by the recent departure of Jay Bennett. Jorgensen’s keys breathe buoyancy into the defiant rocker “Theologians” and adorn “Hell Is Chrome,” Tweedy’s smoldering confession of dancing with the devil, with a rich low end worthy of Talk Talk’s Spirit of Eden. He also wrote the latter song’s elegant 20-second piano intro, which this set reveals was an entirely different composition called “Two Hat Blues” until Tweedy cleverly tacked it onto the top.

That’s one juicy tidbit of many unveiled by this expanded edition, which includes four LPs of alternates and outtakes. There are early trials of songs from the album’s more laid-back follow-up, Sky Blue Sky, including the non-album single “The Thanks I Get,” here with a five-chord piano flourish curiously similar to the one that kicks off “Handshake Drugs.” We learn that “Muzzle of Bees” nearly had a fast-strummed, “Tangled Up in Blue”-style riff. “Panthers,” which originally loomed over the A Ghost Is Born Tour EP like an inbound storm front’s pattering drizzle, is included in the sparer acoustic form that Tweedy recently teased in his “Starship Casual” newsletter. Together, these little artifacts create a detailed snapshot of a band wading almost alarmingly deep into the weeds. They would devote themselves to lengthy experimental songwriting exercises, such as this box set’s three-plus hours of “Fundamentals,” in which Tweedy isolated from the rest of the band, who then played by three rules: that Tweedy could only hear himself and Kotche, that everyone else could hear everything, and that they would all do whatever they wanted. The results are, predictably, wild and sometimes harsh, but full of loose threads for the Wilco heads to connect.

They also left at least one previously unknown jewel off A Ghost Is Born. Until now, “Diamond Claw” was known only as a slow and pretty instrumental from the Wilco Book companion CD that Jorgensen called his “favorite piece of recorded sound that came out of the sessions.” Here, we find that it was also a fully formed pop song with a totally different sound from that version. With a breezy, uptempo drumbeat and a bright melody that fittingly touches on angels and dreams, it stands among “A Magazine Called Sunset” and “Cars Can’t Escape” as Wilco’s best buried pop-rock gems that might have become the “One Headlight”-level hit that their previous label Reprise so badly wanted, if only Tweedy had found any of them to be fit for a studio album.

Opposite such hooks is A Ghost Is Born’s more mischievous anti-pop flipside. “I’m a Wheel” is a gloriously smirking surge of choppy, Replacements-spirited punk rock that sticks out like a forehead zit Tweedy added to his own self-portrait; its lyrics include “uh,” “um,” and “One, two, three, four, five, six, seven, eight, nine/Once in Germany someone said nein.” (Tweedy would occasionally calm his brain by writing out every number from one to 1,000 on gridded pages, which bookend these liner notes as they did The Wilco Book.) The more controversial, penultimate “Less Than You Think” consists of a fragile three-minute piano ballad followed by 12 minutes of each band member holding their own individual drones in unison—Tweedy’s sonic description of a chronic migraine. That part isn’t for everyone, but it works as a savvy, creative form of punctuation for a vulnerable moment. Such a sorrowful song—about finality, free will, and God raising a toast to lightning—earns an unreasonably massive echo chamber. Once accepted, it’s actually a calming and welcome pause, like 12 blank pages between a great book’s last two chapters.

The album ends with one final twist, as the band whirls from its most artsy to its loosest with a shining gold nugget of jangle in “The Late Greats.” Here, Tweedy gives it up for the singers, songs, and bands that deserved to make it big but never did. “Romeo,” “Turpentine,” and “The Kay-Settes Starring Butchers Blind” are all fictional, but the music that they represent—and these lyrics certainly bear some likeness to how Tweedy once described “Before Tonight” by the Illinois alt-country band Souled American—might be the album’s implicit dedication. A second straight Wilco album winds down with the radio on Tweedy’s mind:

The best songs will never get sung
The best life never leaves your lungs
So good you won’t ever know
You’ll never hear it on the radio

A Ghost Is Born would win Wilco’s only two Grammys, including Best Alternative Album. After learning they had won, they opened their show later that night with “The Late Greats.”

A Ghost Is Born’s most interesting distinction, however, is that it remains the only Wilco album with Tweedy as lead guitarist—originally by necessity, after Bennett’s departure, and later at O’Rourke’s emphatic encouragement. What comes through Tweedy’s electric is more kinetic and less compelled toward traditional technique than Bennett and Brian Henneman before him, or Nels Cline after. What his soloing lacks in grace or slick licks, it makes up for in honest reaction, bending around several notes of a motif one second, then shattering into a spur-of-the-moment tremolo the next. He never strays too far from the melody, and he stumbles well, as if refusing to go down while his knees wobble beneath him. On opener “At Least That’s What You Said,” his freaked-out Gibson SG chases the wayward winds of Neil Young’s “Like a Hurricane” after the whole band indulges an eight-bar slam dance of staccato quarter-note mashing. Temporary relief arrives with the warm buzz of “Handshake Drugs,” an enveloping highlight of both the album and its outtakes here, in which Stirratt and Kotche’s brilliantly patient rhythm track thumps along with rock-solid consistency under Tweedy’s sweat-dampened squall, like the earth rotating on in content oblivion while a narrator slips away from a moment’s peace.

And as far as those solos go, there’s nothing quite like “Spiders (Kidsmoke),” the album’s best song. “Spiders” was yet another that was workshopped in several forms—the more acoustic, pastoral version from a February 2002 outtake here has also shown up frequently at Wilco and Tweedy solo performances ever since—before eventually landing on this eerie krautrock dream of Neu!’s “Hallogallo” in a blender with Suicide’s “Frankie Teardrop.” Three cycles of piercing tension from Tweedy’s highest, most tightly wound strings result in inevitable snapping. His guitar staggers around a pre-chorus phrase with sustained distortion, then eventually gains balance, sharpens up, and throws a haymaker of a power-chord sequence with his band behind him in perfect lockstep. The instrumental chorus is strong enough without any words, but Tweedy’s worn groan enters the third time around to finish the job with equal determination and defeat: “There’s no blood on my hands/I just do as I am told.” At over 10 minutes, it challenged his ability to stave off his headaches and remain standing for the whole recording. “We attempted two takes and take one is the one on the record,” he wrote in his memoir. “Take two was incomplete.”

Since then, Tweedy has never struggled so seriously with his health while making an album. Between finishing A Ghost Is Born and entering a dual-diagnosis clinic, he would recruit the journeyman guitarist Cline and Stirratt’s co-bandleader in Autumn Defense, multi-instrumentalist Pat Sansone, to join Wilco. Bach would accomplish probably the cleanest exit in band history, bowing out after recording to settle down in his hometown of Chicago, where to this day he supports and collaborates with local artists including Marvin Tate and Official Claire. Tweedy, Stirratt, Kotche, Jorgensen, Cline, and Sansone have been the six members ever since. The A Ghost Is Born tour was their first together, where they fine-tuned both the new material and the back catalog, as heard on the excellent 2005 live album, Kicking Television: Live in Chicago.

This was the iteration of Wilco that my 16-year-old self fortuitously discovered after wandering over to a big stage at a summer music festival: sturdy, reinforced, giants of live performance whose frontman sported what Stirratt would teasingly call a “Bob Dylan beard” (which soon became the namesake of a fantastic folky deep cut included in these outtakes). It’s also where this box set ends. The last piece of this expanded edition is a live recording of a Wilco concert at Boston’s Wang Center in October of 2004, shortly before that year’s presidential election. In its closing moments, Tweedy notes the stakes, then jumps into the Woody Guthrie-penned “Christ for President,” then is told that his band has been encoring for too long. He leaves the audience with three words paraphrasing a Bill Fay song that helped get him through his toughest times, a message that A Ghost Is Born would in turn offer to so many: “Don’t be scared.”