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By Matthew Reisen / Journal Staff Writer Friday, September 23rd, 2022 at 7:17PM

A former ROTC instructor charged in the rape of a 16-year-old Shiprock High School student with special needs is now alleged to have raped another teen — getting her pregnant — while working at the school late last year.

A search warrant affidavit unsealed Thursday laid out the new allegations against Ira Harris after a mouth swab was taken from the 55-year-old to be compared with the DNA of a baby born earlier this month to a teenage girl in Shiprock.

Harris is already facing federal charges of engaging in a sexual act with a person incapable of appraising the nature of the conduct, knowingly receiving or distributing child sex abuse material and tampering with a victim in a separate December 2021 rape.

He has been released on pretrial conditions with a GPS monitor on those charges. Harris’ attorney could not be reached for comment.

Officials said Harris was placed on administrative leave when allegations surfaced in January and resigned on Feb. 6. He has worked in the ROTC program at Shiprock High School since 2015.

The school’s website lists Harris as the senior Marine instructor of the ROTC Chieftain Company and says he is a retired master gunnery sergeant with the U.S. Marine Corps. A photo on the website shows Harris posing with the Junior ROTC class as they showed off multiple trophies from a 2019 championship.

The Navajo Police Department was alerted on Jan. 19 to the rape of a 16-year-old student by her ROTC instructor Harris, according to a criminal complaint filed in U.S. District Court. Authorities found explicit messages between Harris and the student on her personal tablet.

Authorities said the girl has a learning disability, an IQ of 60 and suffered a psychotic episode at school in October 2021. In that episode, Harris helped officials convince the girl to be hospitalized.

On Dec. 17, according to the FBI, Harris and the girl made a plan for her to sneak out of her house and he picked her up in his truck. The girl told agents Harris raped her before relatives found the pair and took the girl home.

Authorities said DNA evidence taken from the truck proved the two had sex.

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Agents found messages from Harris, sent in January after the investigation began, telling the girl his life was ruined and he was going to jail because she didn’t delete their messages, according to the complaint. Authorities said Harris told the girl police took all of his guns because they thought he “might hurt himself” and says he gave suicide “some serious thought.”

Authorities said they found at least one naked photo of the girl on Harris’ laptop and he “had firsthand knowledge” of her “limited cognitive abilities and sensitive mental conditions.”

“Her inability to consent, understand consequences, or make mature decisions was apparent,” according to the complaint.

Then, according to a search warrant affidavit filed in U.S. District Court, agents were notified Aug. 26 of a 15-year-old who became pregnant while a member of ROTC under Harris’ tutelage. The girl, who had “similar learning disabilities” to the other victim, told agents the father was “a much older man,” that she was forced to have sex and it occurred in Shiprock.

The girl had a baby boy on Sept. 11, and a mouth swab was taken from the infant and from Harris for comparison, according to the affidavit. The results of the test are not given in the affidavit but agents believe Harris is the father due to the similarities between the teens with “learning disabilities, a history of physical and sexual abuse, and inconsistent home life.”

Agents said the teens also admired Harris, who served as “an authoritative figure” for both.