"The motive is fundamental," attorney Carlo Dalla Vedova told the jury in Perugia, Italy, where Knox has been jailed for the last two years. "But today the motive has been changed at the last minute."
During a preliminary hearing, prosecutors claimed that Knox and two men slit Kercher's throat during a sex game gone awry. Prosecutors said during their summations last week, however, that Knox wanted revenge on her "prissy" roommate for criticism over being sloppy and bringing boys back to their apartment late at night.
Prosecutors have asked that Knox be sentenced to life in prison and be ordered to pay $12 million in damages to Kercher's family.
"At the very end of the trial the prosecution has changed the motive, not in the course of the trial and supporting it with evidence," Dalla Vedova said. "It is no longer the result of a sex party gone wrong. Now it is Amanda who organized the crime out of vengeance."
He noted that seven of Kercher's friends testified that Kercher had criticized Knox for her cleaning habits, for her guitar playing, because she brought boys home - the usual problems that come up when girls live together.
"And yet it is from this hate that everything else is meant to follow - according to the prosecutor, it is all Amanda, Amanda against another girl," Dalla Vedova said.
"You have to explain the hate to me. Where is it?" the lawyer asked. "This cannot be used as evidence."
Dalla Vedova, speaking on the second day of summations for the defense, said in the days after Kercher's body was found on Nov. 2, 2007 in the cottage they shared, Knox didn't flee, despite offers of a haven from the violence by family members at home in Seattle or in Germany.
"Amanda stayed in Perugia, she did not run away. She did not go to Germany when her aunt told her to come. On the morning of the 5th, the day she was interrogated, she went to school. She wanted to be in Perugia," Dalla Vedova told the jury.
Knox, he said, was a "clean-faced young girl. I know her well. And she was swept away by a tsunami" of events.
He described the police investigation as an "incredible evolution of facts that led to the arrest of Amanda Knox. It was a sort of rush."
The lawyer said police looked at Knox as a suspect because she behaved oddly in the days after the murder, including doing a cartwheel in a police station while waiting to be questioned, behavior he explained by saying she as "a girl who was alone on the other side of the world from her family."
"She became a suspect based on her behavior... They called her an assassin based on the fact she did a cartwheel," Dalla Vedova said.
"It was a mistake from the beginning. Police focused on Amanda and they were wrong," he said.
He disputed the impression that Knox was cold and uncaring while at the police station in the days after the Kercher's murder. He quoted the testimony of a court interpreter who said that on Nov. 4 she saw Knox in a waiting room at the police station. The witness, said Dalla Vedova, said Knox was pale, and looked ill and the interpreter was worried about Knox who said that she had not eaten or drunk anything all day.
Knox's lawyer also reminded the court how on that same day Amanda was taken back to the scene of the crime, along with her housemates, and shown the knives in the house. They were asked whether the knives were part of the household cutlery. At the sight of the knives, Amanda collapsed, witnesses said during the trial, and had to lie down.
Dalla Vedova challenged some of the evidence presented by prosecutors, particularly the claim that a knife found in the kitchen of Knox's co-defendant and former boyfriend Raffaele Sollecito had a speck of Kercher's DNA on the blade and Knox's DNA on the handle. Prosecutors claim the knife is the murder weapon.
During the trial, Knox's lawyer presented forensic experts who argued that the blade of the knife was not compatible with the cuts on Kercher's neck, and there was too little DNA to carry out a second test to confirm the DNA.
"The compatibility of the knife... how can you evaluate the evidence of the knife?" Dalla Vedova asked. "It is not strong enough to be proof."
Noting that Kercher's DNA on the knife did not include blood, he demanded, "How can you use it as a murder weapon and not find blood on it?"
He also warned the jury to not be influenced by the widepsread coverage of the murder and subsequent trial in the Italian press.
Knox, he said, "has been the object of a trial through the media, of slander, of violation of privacy... You have to keep in mind the great influence of the press on this trial."
During a break in the day's proceedings, Knox's father Curt Knox told ABC News that he was pleased with the summation.
"I think it's going well. Carlo is trying to emphasize to the jury they need to separate the public media trial from the trial in the courtroom. Look at the facts and what is heard in the courtroom, not outside," Curt Knox said.
"Amanda is as confident in her attorneys as we are. We look forward to seeing a positive result," he said.
The knife as evidence also came under attack outside the courtroom today. Elizabeth Johnson, a forensic biology and DNA expert, has co-authored a petition stating that the knife proves nothing.
Johnson told "Good Morning America" today, "The handle of the knife is expected to have some of Amanda's DNA on it since she used those kitchen knives to prepare food in Raffaele's apartment."
She dismissed the DNA on the blade saying, "It's an amount of DNA that would come from 20 or fewer cells.... The key part of this is there was no blood detected by chemical test methods."
"That test, when the handle and the knife blade were tested with chemical tests, were negative when tested for blood," said Johnson, who has not examined the evidence.
She also criticized the DNA tests on Kercher's bra clasp that was torn loose during her murder and not recovered by police until weeks after they searched the house. Sollecito's DNA was found on the clasp, which prosecutors argue puts him at the scene of the murder.
"That bra clasp was found and collected 47 days after the murder. And it had been moved from its original location where it was documented on the crime scene video," Johnson said.
"These DNA results could have been obtained even if no crime had occurred," Johnson said, saying the DNA could have transferred in the bathroom or in laundry.
Johnson said there was "absolutely not" enough evidence to link Knox to the crime.
In the courtroom, Dalla Vedova also lashed out the prosecution's demand that Knox be sentenced to life in prison.
"Remember," Dalla Vedova said, "that life in prison is the most severe punishment in our country. There is nothing worse that what the prosecutor has asked for Amanda."
But with the long trial coming to an end, he said, "Doubt remains in this trial today, and a young girl is waiting to be judged."
"The truth comes out in a trial, and we have been waiting for this moment with patience," he said. "Especially Amanda Knox, who has been waiting in jail with great patience and determination, waiting to get her life back.
The jury is expected to get the case Friday.