Cummins, who reportedly said "I'm glad this is over" upon his arrest, is facing both state and federal charges including aggravated kidnapping, sexual contact with a minor, and taking a minor across state lines for sex.
Cummins and Thomas disappeared on March 13, sparking a cross-country manhunt made all the more hard as Cummins apparently changed his appearance and may have switched out the license plate on the vehicle he was driving, according to reports.
Thomas was found safe with Cummins after local residents tipped authorities to the presence of the pair late Wednesday night, Giordano said.
One of the email drafts shared with WAAY begins with Cummins telling Thomas that he "saw you standing next to you [sic] backpack this morning". He was added to the state's most wanted list.
"At the end of the day she's 15 years old".
Cummins surrendered without incident, according to the TBI. "(Thomas) indicated Cummins may have been consoling her when the student walked in.
The teacher would later be reprimanded on February 3 by school principal Penny Love after the girl was seen in Cummins' classroom for a little more than half an hour that day. Three days later the teacher was suspended.
Cummins, 50, and Thomas, 15, had been on the run since Monday, March 13. Follow-up investigation revealed he never had an interview. She was located more than a month after she was last seen at home in Columbia, Tennessee.
On the morning the pair went missing, the affidavit says Cummins lied to his wife, telling her he had a job interview and needed to borrow her vehicle, the 2015 Nissan Rogue.
"He said he would be back and urged his wife not to call police", the documents state.
That next morning, the caretaker asked Cummins to come outside and help him build a rock wall on the property. "At that time, the wife did not contact police". When they reached out to the Siskiyou County Sheriff's Office, they were informed the same person already called them.
Cummins, 50, fled with Elizabeth, his student, from their small town of Culleoka, Tennessee, on March 13.
The girl's father, Anthony Thomas, had told NBC News that he believed Cummins was grooming the children in his class - telling them lies including that he had previously worked for the Federal Bureau of Investigation and Central Intelligence Agency.
Fact: Investigators were looking into the possibility they were crossing the border.
Surveillance video from Wal-Mart stores in Oklahoma City and Guymon captured video of the student and teacher. That room only had one bed. Further investigation of that tip also led authorities to learn Thomas and Cummins visited another Wal-Mart store March 16, purchasing women's razors, chocolate, cheese cubes and KY Jelly, the report states.
For weeks, authorities have been urging the public to remain vigilant in secluded or off-the-grid areas, as they expected Cummins was keeping Thomas somewhere out of the public's eye.
Kelly Giordano of the Siskiyou County Sheriff's Office out of California confirmed with WKRN that a Nissan Rogue was found in their county.
Authorities are working to reunite Thomas with her family.