On the day Annie Le disappeared, Raymond Clark III reported seeing the Yale University graduate student leave the Yale Animal Research Center carrying a notebook and two bags of mouse food.
But police said she never left the building.
In the days after Le was reported missing on Sept. 8 and before the Sept. 13 discovery of her body, found stuffed into a wall of the research center, police looked closely at Clark. An arrest warrant affidavit released Friday charging Clark with killing Le accuses Clark of trying to cover his tracks by cleaning up the crime scene and hiding potential evidence.
Superior Court Judge Roland D. Fasano last week ordered the arrest warrant affidavit released. The 13-page document reveals what led police to Clark: security key cards that showed the movements of both Clark and Le on Sept. 8, scratches on Clark's body, Clark's apparent attempts to clean up the crime scene and ultimately the discovery of both his and Le's DNA on a green-ink pen and socks found at the scene.
The affidavit does not offer a motive for the strangulation, but sources familiar with the investigation have told The Courant that the crime stemmed from a work dispute between Clark and Le.
Only a small portion of the affidavit - about six lines - is redacted. That information appears to be about the discovery of Le's body.
The affidavit details the movements of Le and Clark on the day police believe Le was killed.
Le, 24, a third-year doctoral student in pharmacology from Placerville, Calif., swiped her key card at 10:11 a.m. in a lab room, G13, at the Yale Animal Research Center on Sept. 8. Clark, a 24-year-old lab technician from Middletown who tended the animals at the research center, wasn't far behind Le, reporting for work at the center 29 minutes later that day, according to the affidavit.
At 11:04 a.m., Clark, wearing blue jeans, white shoes and a dark-colored jacket with white stripes, entered the lab where Le was working and remained there for 46 minutes. He signed in as "RC," using a green-ink pen, the document states.
Clark was busy at the lab that day, according to key-card activity that shows a person's movement in, out and throughout the center, a state-of-the-art secure building that is part of the Yale School of Medicine complex.
From 10:40 a.m. that morning until 3:45 p.m., Clark went in and out of the lab room where Le was working and another room, G22, down the hall 55 times, according to the documents.
When he left the building that day, Clark was seen wearing different clothes from the ones he entered wearing.
Le, however, was never heard from again.
By 11 p.m. Sept. 8, police were already wondering what happened to Le, who was looking forward to marrying her college sweetheart that Sunday in a lavish Long Island wedding.
Le's roommate, Natalie Powers, who shared an apartment with Le in the city's East Rock neighborhood, called police when Le failed to return home the evening of Sept. 8.
During an interview with Powers at her Lawrence Street apartment, Yale University police learned Le never called Powers that day, which was "very unusual" for her roommate and friend.
By all accounts from Le's family and friends, the friendly and smart 24-year-old was excited about her upcoming wedding. Rumors about her being a runaway bride soon turned into concern about Le's safety.
New Haven police, state police, and the FBI joined the search for Le. Immediately, they turned to the research center and the building's electronic video surveillance. It showed Le entering the research center at 10 Amistad St. at 10:09 a.m. Le's electronic key card log for that day showed her card was used to get into the lab at 10:11 a.m.
When both Le's key card and video surveillance cameras - which are posted in all of the building's exits, according to the FBI - showed that Le never left the building, investigators began an all-out search inside the research center, interviewing Le's co-workers and other employees who may have seen Le.
Yale student Rachel Roth, one of Le's co-workers, told Yale University police Officer Sabrina Wood about a box of wipes with blood spots on it.
The box was on a steel push cart inside the last room Le logged into Sept. 8.
But the blood on the wipe box wasn't the only thing that captured Wood's attention.
While waiting for FBI agents one day during the search for Le, Wood said, she saw Clark go in and out of the lab. At one point, Wood said, she saw Clark go over to the cart and move the box of wipes so the "blood splatter was facing ... away from plain sight." Clark then made "small talk" with Wood, according to the affidavit.
"The action of Clark, as observed by Officer Wood, appeared to be a deliberate attempt by Clark to block her view of the box in question," the affidavit states.
As investigators searched for Le, Clark continued to work in the lab, scrubbing the floor drain with steel wool and cleaning solutions. Wood would later tell investigators she thought the cleaning was unusual because the drain was already clean.
But the cleaning didn't end there. Clark was also seen by Yale police Sgt. Jay Jones scrubbing the floor under a sink, near the drain. Jones said he thought it was unusual because he said the floor did not need to be cleaned, the affidavit states.
Jones said he also saw Clark "make contact" with the push cart.
By Sept. 10, the FBI had collected a list of evidence, including the box of wipes and an extra-large lab coat with red stains from a recycling box.
Video footage showed Clark wearing a similar lab coat Sept. 8, according to the affidavit. The evidence was taken to the state police forensics lab, where scientists extracted DNA from the items.
Meanwhile, detectives went back to Le's Lawrence Street apartment to gather items to use to extract Le's DNA, including her toothbrush.
Results from those tests showed that Le's DNA was on the box of wipes and on the lab coat. Scientists also detected an unknown male's DNA on the lab coat collar and cuffs.
Also on Sept. 10, Clark came forward with information about Le. He told Yale police Officer Jennifer Garcia he saw Le leave the building at 12:45 p.m., 15 minutes before he left the building and before a fire alarm went off in the building. The alarm was activated by steam from an autoclave used to sterilize lab equipment, the affidavit states.
In interviews with investigators, Clark said he met Le sometime in early 2009. He told detectives he did not socialize with Le and never had contact with her outside of work.
He said he reported to work Sept. 8 at 7 a.m. About 10:30 a.m., Clark said, he saw Le, dressed in a brown skirt and yellow lab coat, doing work in the lab. Between 12:30 and 12:45 that afternoon, Clark told police, Le left the lab carrying a notebook and two bags of mouse food.
During the interview, police asked Clark about scratches he had on his face and left biceps. He told them the injuries came from one of his cats.
The interviews were enough to convince investigators to take a closer look at Clark. They applied for search and seizure warrants to get mouth swabs, body hair, fingerprints and fingernail clippings from Clark so they could compare the evidence to what was found at the scene.
On Sept. 12, detectives got a break - evidence was discovered above a hallway drop ceiling outside the lab. Police found a bloodstained rubber glove and a sock. That evidence was collected along with blood-covered work boots labeled "Ray-C," a blue hospital scrub similar to a shirt Clark is seen wearing in video surveillance, and other items.
Investigators also found bloodstains in lab rooms that someone "attempted to clean," according to the affidavit.
Though much evidence was seized, police had yet to find a body.
But on Sept. 13, just hours before Le was to be married, a foul odor emanating from a lower-level locker room captured the attention of an investigator, the affidavit states.
Police dogs brought into the building found the "lifeless body of a female." She was wearing surgical gloves with her left thumb exposed. Blood was smeared behind the wall and insulation was used to attempt to conceal the body. Detectives found three key items inside the hiding space: a green-ink pen, a bloodstained lab coat, and a sock similar to the one found in the hallway drop ceiling.
At that time, investigators examined Clark's movements in the building on Sept. 8.
They discovered that Clark's key card activity was "substantially higher in comparison to his prior use," according to the affidavit.
On Sept. 15, police searched Clark's Middletown apartment and took samples from him in an effort to obtain his DNA.
According to the warrant, police got the match they needed to make an arrest. On the green-ink pen, investigators found a bloodstain that contained Le's DNA, and they found Clark's DNA on the pen cap, the warrant states.
A stain on the sock found above the ceiling tile contains "a mixture of both Raymond Clark's DNA and the victim's DNA," the affidavit states.
Clark was arrested on Sept. 17 at a Super 8 Motel in Cromwell. He is charged with murder.
Clark is being held, with bail set at $3 million, at the MacDougall-Walker Correctional Institution in Suffield. He is due back in court Dec. 21.