A Flathead District Court judge ordered a psychological evaluation Thursday for a man charged with kidnapping after a six-hour standoff at a Kalispell motel on New Year’s Eve.

Thomas Mulligan, 36, was brought before Judge Stewart Stadler after submitting a handwritten letter in which he indicated his desire to represent himself in court and plead guilty to two felonies.

Mulligan has been charged with kidnapping and criminal endangerment by the Flathead County Attorney’s Office.

He was arrested Dec. 31, 2010, when the Kalispell Police Department SWAT team stormed his Super 8 motel room and found him barricaded in the bathroom with a 17-year-old boy.

Police say he met the youth on the Internet several months before and that the two were traveling in a vehicle reported stolen in Filer, Idaho.

Mulligan allegedly threatened to kill himself and the youth when law enforcement initially came to his room after locating the stolen vehicle in the parking lot.

Glen Neier, Mulligan’s attorney, said Thursday that Mulligan likely will be indicted in federal court for alleged crimes committed in Idaho.

Mulligan indicated that his desire to plead guilty to the charges — which carry combined maximum penalties of 20 years in prison — is based on his fear of the federal prison system.

“I’m afraid of that situation and I’d rather be in any other state,” Mulligan said.

Stadler said Mulligan’s letter to the court raised issues about Mulligan’s mental capacity. He noted that the letter referred to people being held underground and tortured.

“Some of what you said in these letters concerned the court that you might have some mental health issues,” Stadler told Mulligan.

Stadler told Mulligan that even if he were to plead guilty, he would be placed in federal custody to face any additional charges after serving his sentence, which could be shortened to as few as  2 1/2 years.

“At least it would be two and half years longer without being in the federal system,” Mulligan said.

Stadler said he would be willing to consider Mulligan’s requests if a psychological evaluation deems that he is competent.