PERUGIA, Italy – From the beginning, it was a case of contradictions, and the questions did not end with the verdict that freed Amanda Knox.

The acquittal of the American and her ex-boyfriend in the murder of her British roommate left open the core mystery of whether anyone — other than the lone man still behind bars — took part in the brutal killing.

But it also begged questions that stretch back to the early days of the investigation into the 2007 death of Meredith Kercher.

Why did Knox initially tell prosecutors she was in the apartment that night and had to cover her ears to drown out her friend’s screams as she was brutally attacked by a man Knox falsely accused?

There was also a purported burglary at the apartment that night — staged, prosecutors alleged, by the killers to derail the investigation. Who staged it and why?

And then there was the alibi of Knox’s ex-boyfriend, Raffaele Sollecito, whose conviction was also overturned Monday. He claimed he was at home working on his computer the night of Nov. 1, 2007, yet police testified there was no sign he had used it that evening.

Monday’s verdict, reversing Knox and Sollecito’s 2009 murder convictions, didn’t answer any of those questions. And it’s unlikely the appeals court’s written explanation of its decision — due within 90 days — will shed much light, likely rendering the sensational case a mystery for years to come.

On the core question of who killed Kercher, there may yet be further legal wrangling.

A third defendant, Rudy Hermann Guede of the Ivory Coast, was convicted in a separate trial of sexually assaulting and stabbing Kercher, and his 16-year prison sentence — reduced on appeal from an initial 30 years — was upheld by Italy’s highest court in 2010.

Guede, a small-time drug dealer, acknowledged he was in Kercher’s room the night she died but said he didn’t kill her. Guede said he believed Knox and Sollecito did, but offered no evidence to back up his claim.

The high court ruling upholding his sentence said Guede didn’t act alone, though it didn’t name Knox or Sollecito as his accomplices.

“The courts agree he wasn’t acting alone,” the victim’s brother, Lyle Kercher, told a news conference Tuesday. “If those two are not the guilty parties, then who are the guilty people?”

Guede’s lawyer Valter Biscotti told The Associated Press he would seek to reopen the case for his client in light of the acquittals of Knox and Sollecito.

During his appeals trial, Guede claimed he heard Kercher and Knox argue minutes before the Briton was slain in the apartment they shared.

He said he was at the house with Kercher when he fell ill and went to the bathroom with his iPod. He heard Knox and Kercher argue over money, then heard a “very loud scream” coming from Kercher’s bedroom, and rushed to it. There, he said, he saw an unidentified man who tried to attack him. Backing into the hallway, Guede said he heard the man say, “Let’s go. There’s a black man in the house.”

Knox initially told prosecutors that she was home the night of the murder and had to cover her ears against Kercher’s screams while she was attacked by Diya “Patrick” Lumumba, a Congolese man who owned a bar where Knox often worked.

In the November 2007 ruling ordering Knox and Sollecito jailed, a judge cited that account, but noted that Knox’s memories were confused since she had smoked hashish earlier in the day. Knox didn’t explain why she didn’t try to help Kercher, and subsequently changed her account.

In her final appeal to the court on Monday, Knox said she had been “manipulated” during her police interrogation. She previously accused police of beating her — a claim that landed her another indictment on slander charges, a case that remains open.

The DNA evidence used to place Knox and Sollecito at the scene of the crime during the first trial was determined to be unreliable by a court-ordered independent review during the appeal. But that wasn’t the only testimony purportedly placing them at the scene.

In addition to Guede’s testimony and Knox’s own initial statement, a homeless man testified for the prosecution that he had seen Knox and Sollecito near the apartment the night Kercher was killed.

The defense insisted his testimony was unreliable, and the witness damaged his own credibility by admitting on the stand to being a heroin addict.

Knox changed her account of her whereabouts. She and Sollecito concurred they were at his apartment the night of the murder, though Sollecito said he wasn’t sure if she spent the whole night with him. Knox maintained they had smoked hashish, watched the French film “Amelie” and made love.

Prosecutors also claimed the apartment was unnaturally cleaned of any traces of Knox’s presence. The only fingerprint belonging to Knox was on glass, while many more traces were left by two other Italian flatmates and visitors, they said.

There remains no motive for the killing and questions even swirl about the murder weapon.