Throughout the trial the defense team disputed most of the prosecution's key evidence, including the alleged nod, the surveillance videos and the DNA samples taken from the toll ticket that Chris was alleged to have touched when driving on route to his parent's house on the night of the attacks. The crux of its case hinged primarily on the testimony of ten defense witnesses and the cross-examination of most of the prosecution's 75 witnesses. They hoped that by discrediting earlier testimonies, they would be able to create enough reasonable doubt to acquit Chris of the crime.
One of the main issues that the defense team focused on was that concerning Joan's response to Detective Bowdish's questions at the scene of the crime. The defense suggested that the injuries Joan sustained and the reduced amount of lighting in her bedroom would have made it extremely difficult, if not impossible, for her to identify her attacker. Moreover, they suggested that the significant brain trauma from which she suffered would have greatly impacted her ability to understand or respond appropriately to any questions asked of her after the horrific event.
Dr. Mary Dombovy, one of Joan's neurologists who testified in support of the defense's contention, confirmed that Joan's injuries would have likely prevented her from identifying her attacker and would have hindered her ability to respond to questioning. Elizabeth Harness, a medical reporter for WROC News Channel 8 in Rochester, interviewed Dombovy and quoted her as saying, "There was no real verification that she (Joan) could use yes and no correctly, many people use them incorrectly after a brain injury or have a bias towards one or the other." Dombovy also statd that Joan suffered from amnesia due to the blunt force trauma to her head and would likely never remember the events that occurred during or several weeks after the attack.
At trial, the defense team also questioned the reliability of DNA evidence, which the prosecution claimed implicated Chris in the attacks. William M. Shields, a biology professor who specializes in animal behavior and genetics testified for the defense and suggested that there was less than a 30 percent chance that the DNA abstracted from the toll ticket belonged to Chris, "meaning the DNA could have belonged to more than 70 percent of the population, " The Union Times reported. Shields believed that the DNA analysis was flawed, thus potentially discrediting the evidence.
During the proceedings, the defense team also took aim at the video surveillance footage in an attempt to discredit the prosecution's theory that Chris drove to his parents' house on the night in question. According to the defense, Chris did indeed drive his jeep off campus, as the jury saw in the video footage shown in court. However, they claimed that he only moved his car to another location so as not to incur a ticket. They suggested that the prosecution only speculated that Chris went to his parents' house on November 14th, since there was no video footage that depicted him doing so.