By M. Alex Johnson, NBC News

Arapahoe County District Judge William Sylvester determined that there was probable cause to continue the case, telling Holmes he was accused of having killed 12 people and wounded 58 others early Friday in a crowded theater was showing the premiere of the new Batman movie, "The Dark Knight Rises."

Sylvester set a hearing on formal charges — expected to be 12 counts of first-degree murder — for next Monday at 9:30 a.m. (11:30 a.m. ET). Holmes, wearing a red prison jump suit, said nothing during the hearing. He mostly looked down at the table under a shock of dyed bright red hair and occasionally raised his eyebrows in a quizzical expression.

Relatives of some of the victims leaned forward to catch their first glimpse of Holmes. Some stared at him the entire hearing, including Tom Teves, the father of Alex Teves, who was killed in the shooting. Two women held hands tightly, one shaking her head.

Afterward, he was led away in handcuffs to his cell, where he is being held in isolation, said Carol Chambers, district attorney for the 18th Judicial District, which includes Arapahoe County.

Six-year-old girl, sailor, aspiring broadcaster among Colorado shooting victims

Asked about the seemingly overwhelming evidence that investigators had amassed against Holmes, Chambers cautioned that "there is no such thing as a slam-dunk case."

"We will work very hard on this case just as we would on any other case," she told reporters after the hearing. 

From here, the case could wind on for months or even years.

Will James Eagan Holmes ever face trial?

"A case like this involves so many different aspects — (prosecutors will) be working with the police, dealing with things such as search warrants, locations, is there enough evidence to proceed," James Peters, a former Arapahoe County prosecutor, told NBC station KUSA of Denver. Peters won the conviction of a man who killed killed four people at an Aurora restaurant in 1993. 

Aurora Police Chief Dan Oates said it could take months simply to determine a motive. He said police were working with FBI behavioral analysts.

Then the state must decide whether to seek the death penalty.

Chambers wouldn't say whether prosecutors intended to pursue that option. A capital case would "impact the victims' families for years, and we would want to get their input on that," she said.

Chambers is term-limited, which means that decision could be made by Chambers' successor, Republican George Brauchler or Democrat Ethan Feldman, one of whom voters will elect in November.

Holmes' defense strategy could delay a resolution even longer. If Holmes were to plead not guilty by reason of insanity, or if his attorneys were to argue that he is incompetent to stand trial, proceedings could stretch for years — perhaps  indefinitely.

A defendant is considered incompetent if he's unable to understand the charges against him or to assist in his own defense. Legal proceedings must stop until the defendant is restored to competency.

Scott H. Robinson, a prominent Denver criminal defense attorney, said Holmes' lawyers might have no choice.

If they believe their client is incompetent, they have "an absolute duty to raise competency and [request] a competency evaluation," he said.

Grad school status used to get hazardous materials?
On Sunday, officials at the University of Colorado-Denver Anschutz Medical Campus were looking into whether Holmes used his position in a graduate program to collect hazardous materials, but school officials weren't saying whether they knew he was anything more than a hard-working student.

Police have said that Holmes began buying guns at Denver-area stores nearly two months before Friday's shooting and that he received at least 50 packages in four months at his home and at school.

The university said it was cooperating with police in the case — one of the few comments it has made in the three days since the massacre. It remained unclear whether Holmes' professors and other students at his 35-student Ph.D. program noticed anything unusual about his behavior.

His reasons for quitting the program in June, just a year into the five- to seven-year program, also remained a mystery.

Holmes recently took an intense, three-part oral exam that marks the end of the first year. Those who do well continue with their studies and shift to full-time research, while those who don't do well meet with advisers and discuss their options, including retaking the exam. University officials wouldn't say whether he passed, citing privacy concerns.

The university said Holmes gave no reason for withdrawing, a decision he made in June.

Shocked Aurora vows, 'We will not forget' victims of theater shooting rampage

Holmes wasn't allowed access from the institution after his withdrawal, which was "standard operating procedure" because he was no longer affiliated with the school, said Jacque Montgomery, a spokeswoman for the medical school. Holmes had no contact with university police, she said.

NBC station KUSA of Denver and The Associated Press contributed to this report.