On April 14, 2005, the police arrested McCowen at his home in Hyannis. He was then charged with first-degree murder, aggravated rape and armed assault. The Associated Press quoted District Attorney Michael O'Keefe, who said that investigators had a motive. Initially, investigators refused to disclose what McCowen's motive was or any related information obtained during his nearly seven-hour long interrogation by troopers. However, when the information blockade was eventually removed, what was revealed did more to confuse than clarify the events surrounding McCowen's alleged role in the murder.
During the first part of his interrogation, McCowen said that he never met Christa or visited her house, except to pick up garbage on his regular route. Then, when further interviewed by Trooper Christopher Mason, McCowen's story began to change. Harriet Ryan of Court TV reported that "the turning point of the interview came when he handed the suspect a state crime laboratory report matching his DNA to semen and saliva found on the victim's body," which prompted McCowen to admit that "it could have been me."
Ryan reported that during McCowen's interrogation, he "offered eight increasingly incriminating versions of the crime," most of which included his having had consensual sex with Christa, which he described in great detail. Even though his story changed significantly throughout the interview, he was consistent in one thing that the murderer was not he, but purported drug dealer and friend Jeremy Frazier. During a pre-trial hearing, McCowen stuck to his story and pleaded innocent to the charges against him. He was held without bail while awaiting trial.
Even though it would take more than a year before the case against McCowan would go to trial, Christa's family refused to sit back and wait. Soon after his arrest, the family began a lawsuit against Cape Cod Disposal Co. for $10 million, for employing McCowen even though he had a criminal record. An Associated Press report suggested that compensation, if awarded, would likely go to Ava.