JAMES EAGAN HOLMES was good at being invisible. He spoke only when spoken to, said little about himself, and spurned his close-knit group of college classmates for a solitary life in his small apartment in a rough section of Aurora, Colo. Holmes' shyness seemed to cut him off from the world, said those who knew him. He was slow to smile in conversations with strangers, seemingly tucked away inside himself. 

But the quiet, awkward man who allegedly went on a killing rampage last week in a Colorado movie theater once seemed bound for big things. A science student from Southern California who won scholarships and internships, Holmes graduated "at the top of the top" from the University of California, Riverside, and moved to Colorado to take the next logical step in a promising academic career: a doctoral program in neuroscience. 

Holmes had procured a highly coveted appointment at the university under a one-year neuroscience training grant from the National Institutes of Health, a spokeswoman for the University of Colorado said. The federal grant pays for six pre-thesis doctoral students in the university's neuroscience program at the Anschutz Medical Campus. Holmes, 24, arrived at the Aurora campus last fall, ready to study how electrical signals transmit sensations and ideas in the brain. He and his five fellow students spent hours each day together in a small conference room. One of them said that Holmes was often the first to arrive, riding from his nearby apartment on a BMX bike. But once class began, he had a habit of daydreaming. "It's like you're interrupting" another train of thought that he was pondering, said the student, who asked not to be named because the school had urged Holmes's classmates not to talk to the news media. 

"I was always trying to get into his head," said another student, who spent dozens of hours in class with the mostly silent Holmes. "If no one had ever said anything to him, he wouldn't have said a word" all year. His fellow students could remember just one personal detail that Holmes revealed without prompting: During a conversation about football, he said he was a San Diego Chargers fan. 

After classes, Holmes was always the first to leave. The others, who bonded during this close and intense experience, assumed he was just sequestered in his off-campus apartment.

"I always just figured he liked being alone," one student said.

IN A SERIES of interviews, neighbors and friends from Southern California and Colorado described the man who allegedly committed one of the nation's worst mass murders as anonymous as a glass of water — more Invisible Man than Joker. He grew up on a pleasant street of Spanish-style tract homes in northeast San Diego. His mother, Arlene Rosemary Holmes, is a registered nurse. News reports and a LinkedIn profile suggest that his father is a software company manager in the area. 

When he was younger, Holmes dabbled in soccer and cross-country, but seemed to give them up for academic pursuits. Breanna Hath, 23, a classmate who graduated from Westview High School with Holmes in 2006, said he had a small group of friends who played video games and were "a little nerdy."

"He was really shy, really quiet, but really nice and sweet," Hath said. 

Another classmate, Brian Martinez, 24, attested to Holmes' willingness to help others. "My good grades are partially thanks to him," said Martinez, who was Holmes' lab partner in chemistry. They collaborated in class, but didn't see each other much afterward: Holmes did not go to parties, and he didn't seem to have a large circle of friends, Martinez said.

Holmes instead spent his time studying, it appears. He earned a scholarship to the University of California, where he continued to excel, graduating in 2010 as an honors student in neuroscience, school officials said. 

"I think he was kind of quirky, just the way you expect smart people to be," said the school's chancellor, Timothy P. White. "Quirky in the sense that he probably had a wry sense of humor. He kept to himself more than he socialized. But he was social. He wasn't a hermit or an introvert. He wasn't a loner."

NEIGHBORS FROM HIS gang-ridden neighborhood in Aurora tell a different story. They describe Holmes as a solitary figure, recognizable as one of the few white residents of a largely Hispanic neighborhood, and always alone: alone as he bought beer and liquor at neighborhood shops, alone as he ate burritos at La California restaurant or got his car fixed at the Grease Monkey auto shop, alone as he rode his bicycle through the streets.

He appears to have sought companionship through the website Adult Friend Finder. On the dating site, a post bears a photo of a man with dyed orange hair who appears to be Holmes. "Classicjimbo" describes himself as "looking for a fling or casual sex gal. Am a nice guy. Well, as nice enough of a guy who does these sort of shenanigans." In another part of the page, he asks, "Will you visit me in prison?"

Some nights, neighbors heard loud music throbbing in his third-floor apartment, and often complained about it. Sometimes they noticed a strange purple light in the windows. At other times, the windows were masked by newspaper.

Holmes struggled through his first academic year at Anschutz; he signed up for a class that explored the biological origins of psychiatric and neurological disorders, and was scheduled to give a presentation on "MicroRNA Biomarkers," according to a class schedule published online. Four months ago, however, Holmes apparently lost interest in neuroscience and allegedly began stockpiling ammunition and explosives. His behavior in class didn't seem to change, though, said his classmates. Then came early June, when all first-year students faced a demanding oral exam. The exam came and went, and the other students didn't hear how Holmes had fared. Then they got word: On June 10, he had sent an email to administrators, saying he was leaving school.

He didn't give a reason, the school said.

WITH HIS ACADEMIC career in tatters, law-enforcement officials said, Holmes began to assemble another plan. He received frequent deliveries at his home and the university, according to police. Over a period of two months, he bought a semiautomatic variation of the military's M-16 assault rifle, a pump-action 12-gauge shotgun, and at least one Glock .40-caliber semiautomatic pistol from local dealers. He also bought and stockpiled 6,000 rounds of ammunition from online sources. Every purchase he made was legal.

On June 25, Holmes emailed Glenn Rotkovich, owner of a local gun range called Lead Valley, asking for an application to join the shooting range. Rotkovich followed up with Holmes within a day or two, calling to inform him when to come to the range for orientation. "I got his answering machine," Rotkovich said. "It was a very bass, very deep-sounding, guttural voice," which Rotkovich called "bizarre or freakish." 

After he called a third time, Rotkovich said his attitude changed. "I don't like this," he said. "So I told everybody, if James Holmes shows up, he's doing nothing before I saw him. Is he weird? Is there something strange about this dude? I flagged it that he had to see me before he gets to do anything." 

The next step, the alleged descent of a shy student into horrific violence, remains mysterious.

ON JULY 20, outfitted with bulletproof helmet, vest, and leggings; a throat protector; a groin protector; gloves; and a gas mask — all black — Holmes carried three of his weapons into a darkened multiplex where a midnight showing of The Dark Knight Rises, the new Batman movie, had just begun. Families and teenagers were packed into the sold-out auditorium. Holmes set off tear gas canisters. He fired the shotgun at the moviegoers; turned to the semiautomatic rifle, firing it until its 100-round barrel magazine jammed; and then kept firing with a pistol. Within minutes 12 people were dead and 58 injured, many critically. Minutes later, Holmes surrendered without incident when police confronted him behind the theater. As he was arrested, according to police, he compared himself to the Joker character in the Batman movies. 

Neighbors, acquaintances, and teachers who knew the suspect found themselves searching for any glimmer that could offer some small clue as to how the quiet man from their memories came to be arrested for such a horrific crime. 

Apart from a speeding ticket, Holmes had no previous encounters with the police in Aurora. He had no history of trouble with the police at college in California. He left no easily identifiable online messages or videos that might offer any insight to his mindset. It also remained unclear how Holmes was able to afford the large cache of weapons, ammunition, and protective gear he had. 

After the shooting at the theater, police discovered a sophisticated set of explosive booby traps at Holmes' run-down apartment. A law-enforcement official speaking anonymously said that a trip wire was set about waist high and that among the hazards found in the roughly 800-square-foot apartment were bullets in jars that were rigged to detonate. And there were about 30 aerial shells, typically used in fireworks, which had been fashioned to be explosive devices. The array had been designed "to kill whoever entered it," said Aurora police Chief Daniel Oates. 

Three days after the massacre, Holmes made his first public appearance as an alleged killer, shambling into a Colorado courtroom with a bearing more like that of a teenage delinquent than the comic-book supervillain he reportedly fancied himself to be. His hair was dyed an uneven and amateurish red. He did not speak during his brief appearance and is refusing to cooperate with investigators trying to learn what motivated the attack. A judge ordered him held without bond. 

Afterward, outside the courthouse, David Sanchez said he had seen evil in Holmes' face. Sanchez's daughter and son-in-law were in the theater that night. His daughter survived without injury. His son-in-law was shot in the right side of his head.

Holmes' eyes were what bothered Sanchez. "Demonic or something," he called them.

"There's something wrong with that man," he said.

This story was compiled from reports by James Dao, Dan Frosch, Jack Healy, and Serge F. Kovaleski in The New York Times, and by Joel Achenbach, David A. Fahrenthold, Thomas Heath, and Carol D. Leonnig in The Washington Post. ©2012 by The New York Times and The Washington Post Co. Used with permission. All rights reserved.