In a small courtroom packed with media, relatives of the dead and injured, and even some of the walking wounded themselves, Holmes sported a shock of dyed orange hair and a prison jump suit.
His hands were cuffed and he did not say a word. He did not seem to look at his victims, either staring straight ahead or looking at his feet. He had been brought into the building via an underground tunnel from a next-door jail, where he is being held in solitary confinement and is on suicide watch.
Holmes seemed dazed and at one point had to be encouraged to stand up, prompting speculation that he was on medication. The brief 10-minute appearance now sets in train what is expected to be a lengthy legal battle as prosecutors prepare a huge charge sheet and defence lawyers mull whether he is mentally fit to stand trial.
Holmes, 24, will be accused of bursting into a midnight screening of the latest Batman movie in the Denver suburb of Aurora, hurling gas canisters and shooting his victims.
He also left behind a booby-trapped apartment filled with homemade bombs. When arrested he reportedly told police he was the Batman villain the Joker, who also has coloured hair.
It was not clear if any of Holmes's family attended the hearing, but a lawyer retained by the family, Lisa Damiani, held a press conference to clarify a remark by the suspect's mother to an ABC-TV reporter soon after the shooting.
Damiani, speaking in San Diego, said that at the time of that early-morning phone call, Arlene Holmes was not yet aware of the attack or accusations that her son was involved.
In telling the reporter, "You have the right person," Arlene Holmes was confirming her identity and not referring to her son, Damiani said.
Damiani said Arlene Holmes' comment to ABC had been misconstrued by some media to suggest that she was not surprised to hear that her son had been involved in the shooting rampage.
For victims in the court, seeing the man who had brought such agony to their quiet slice of suburbia was surreal and upsetting. "I just wanted to see him face to face. He was not able to look at me," said Mckayla Hicks, 17, who was shot in the jaw by a bullet that went through the wall of the theatre and into the next auditorium.
Hicks still has the bullet lodged in her face but decided to come to court anyway as a way of coming to terms with the senselessness of the event. "I feel a lot of confusion and anger, just wondering why he wasted all his talents," she said.
That is a common question in Aurora, and one that has been posed by everyone from ordinary citizens to President Barack Obama, who visited the community on Sunday night and spent several hours with each family whose relatives had died.
The picture that has emerged so far of Holmes is of a lonely, shy person, but a talented scientist, who had grown up in a stable middle-class home in San Diego and been a camp counsellor and an excellent student. "I know people say he was a genius. It is hard to see someone that smart throw it away," said Hicks.
But some victims in the courtroom were less keen on trying to understand what might have been going through Holmes's mind. David Sanchez, whose son-in-law was shot but survived, was visibly upset by being near to Holmes.
"He was pretty crazy looking. There was something not right about him," Sanchez said and added: "Justice would be served for him to get the death penalty."
Holmes's first court appearance likely marks the start of Aurora's process of coming to terms with being the site of such a tragedy. The city has already held an official vigil and service of remembrance at which local officials, victims and ordinary citizens prayed and listened to church choirs sing. "The pain is still raw but we will reclaim our city," said Aurora mayor Steve Hogan.
At the vigil, Colorado's governor John Hickenlooper read off the names of each of the 12 dead and the crowd responded: "We will remember."
But if Aurora has been unimaginably convulsed by the event, so far there is little sign of the shooting sparking any meaningful political debate over the issue of America's relaxed gun laws.
Gun controls have actually grown looser since the 1999 Columbine school shooting – which also happened in suburban Denver just a few miles from Aurora in the city of Littleton.
In his speeches on the tragedy, Obama has spoken of the suffering of the victims and the sense of the shock that has spread across the nation, but has not mentioned any support for tightening gun laws. Less unexpectedly, neither has his Republican challenger Mitt Romney, whose party base is fiercely opposed to any gun control legislation. Only New York mayor Mike Bloomberg has been a rare voice publicly calling for action.
That is of little surprise to leading anti-gun campaigners, including Denver local Tom Mauser, whose 15-year-old son Daniel died in the Columbine shooting. Mauser, who is now a leading voice on stricter controls, said that he believed America was simply in thrall to the gun lobby.
"It is so pervasive in America. This is nothing to do with Colorado. This is to do with America's gun violence, " he told the Guardian. Much has been made of the size of the arsenal that Holmes collected over the past four months and will be accused of putting to grim use inside the movie screening. It consisted of four guns, including a semi-automatic assault rifle, more than 6,000 rounds of ammunition and head-to-toe bullet proof protection. However, all of it was bought entirely legally either online or in person in gun store. There were a few warning signs that with hindsight appear to show a troubled young man. A year ago Holmes had tried to rent an apartment from one Aurora building manager but she turned him down, despite good references and a clean criminal record, because he had seemed unreliable and slightly strange. Then, in recent months, Holmes also alarmed the owner of a local gun range that he had applied to join by having a nonsensical voicemail message. Yet none of that even remotely seemed to suggest that Holmes was planning such a massive assault on a crowded room of strangers settling in to watch a summer blockbuster.