In addition to state charges, which include aggravated kidnapping and sexual contact with a minor, Cummins faces federal prosecution for transportation of a minor across state lines for the goal of criminal sexual intercourse.
Before Elizabeth's disappearance, the school had been investigating Cummins after another student reported seeing him kiss the teen in January.
Authorities said Elizabeth has since been reunited with her family and was being evaluated for emotional trauma.
While they were on the run, federal prosecutors say they went through nine states and that Cummins disabled the Global Positioning System in his vehicle, used aliases and disguises and stayed at low-profile locations on their trip.
As part of his "audacious scheme", Cummins also used a small watercraft to conduct "a test run" for their trip to Mexico, according to the documents.
Cummins, who appeared at an arraignment in Sacamento, walked into court wearing an orange prison jumpsuit that said "Sac Co prisoner" and he was shackled with a chain around his waist.
An Amber Alert was issued for Elizabeth Thomas, 15, after her former teacher allegedly kidnapped her in March.
Cummins was taken into custody Thursday and the teen was placed in protective federal care.
Danielle Thomas said the family's first inclination when Elizabeth went missing was that she had run away.
Bozeman said, "She was abducted and she's grateful to be home". "He surrendered without incident and has been co-operative with investigators".
According to a criminal affidavit filed in support of Cummins' arrest warrant, Tennessee investigators said Cummins - who'd already been suspended by Culleoka Unit School for disobeying orders to steer clear of Elizabeth - stole his wife's vehicle on March 13, falsely told her he was going to Virginia to "clear his head" and asked her to forgive him.
Cummins reportedly "made a number of damaging admissions to law enforcement that provide alarming inside his mentality", the documents states.
A statement was also released by the family's attorney, S. Jason Whatley, on Friday following the reunion. He is awaiting extradition to Tennessee, where he will be charged with sexual contact with a minor and aggravated kidnapping.
Two days after the girl disappeared, surveillance images from a Walmart in Oklahoma City showed Cummins and the girl purchasing food items in the store with cash.
Thomas' father said last week he believes his daughter was "brainwashed" by Cummins.
"Right now, she's somewhere where she can relax and be looked after by family and close friends and just take a break from everybody", Anthony Thomas said.
"He's done this frightful thing that he has to pay for, but he's still my brother and I love him", Quinn told NBC News.