A man arrested in Keene last week after a two-day manhunt was arraigned in court Monday.

Patrick Allen Boyer, 39, of Nelson, pleaded not guilty on nine misdemeanor charges and did not enter a plea for six felony charges in Keene’s district court, where he appeared via video from the Cheshire County jail.

Felony charges include two counts of theft by unauthorized taking, two counts of reckless conduct with a deadly weapon, criminal restraint and second-degree assault with domestic violence and strangling, according to the case summary. In the legal system, a vehicle is considered a deadly weapon.

The misdemeanor charges include three accounts of resisting arrest, two counts of disobeying an officer, two charges of simple assault, two counts of disobeying an officer, conduct after accident and obstructing the report of a crime, per the case summary.

Boyer was arrested by Keene police and state troopers near Walmart in Riverside Plaza on Friday, ending a two-day search, according to State Police Capt. Vincent Grieco. The search began after police obtained a felony warrant Wednesday for Boyer’s arrest after a reported assault.

The charges span four jurisdictions: Keene, Nelson, Stoddard and Sullivan, per the case summary.

As part of a bail agreement, Boyer was ordered not to make contact with an alleged victim, Judge Patrick Ryan said during Monday’s arraignment.

A probable cause hearing, where a judge will determine whether there is sufficient evidence to conclude a crime happened, is scheduled for Wednesday, Sept. 30.

N.H. State Police and its detective bureau were involved in the initial investigation into Boyer’s alleged assault, Grieco said during a news conference Friday. Local departments were issued a “be-on-the-lookout” alert Wednesday evening.

During their ensuing search, police described Boyer as “potentially armed,” but Grieco declined to comment Friday when asked whether there was evidence he was armed. He also would not comment on the identity or condition of the alleged victim in the assault.

Boyer allegedly stole two cars — one in Stoddard, the other in Keene — and engaged police in multiple pursuits by vehicle and on foot, Grieco said. The police did not know Friday how he allegedly stole the vehicles.

While police searched for Boyer Thursday, they advised residents in Nelson and Stoddard to stay in their homes and part of Route 9 was closed. On Friday morning, residents in part of Keene were advised to shelter in place, and a length of Route 9 was closed from its connection to Route 10 in Keene to the Sullivan Country Store.

Schools in N.H. School Administrative Unit 29 — which include Chesterfield, Harrisville, Keene, Nelson, Marlow, Marlborough and Westmoreland — went into emergency protocol for a short time on Friday, according to Superintendent Robert Malay. Keene State College also initiated emergency protocols around 9 a.m., per a college spokesperson.

Boyer was previously convicted in Vermont of sale of cocaine and heroin, felony conspiracy to sell illegal drugs, fraud and involvement in the theft, use or concealment of stolen property.

In 2023, he was sentenced to five to 12 years in state prison on charges of aggravated domestic assault with a weapon, domestic assault and violations of the conditions of release.