The woman told police that Mull was holding her against her will and forcing her to take drugs.
Police say she had visible injuries to her neck and a burn mark from a torch on her back.
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Scipioni reportedly denied having an inappropriate relationship with the student when questioned by school officials in 2010.
The affair reportedly resurfaced in 2014, when Scipioni was going through a divorce.
According to police, the woman said Mull choked her to the point of passing out and raped her.
She also said he threatened her family and friends, and threatened to use her in human trafficking.
The school board voted to appeal that decision to the state Supreme Court in February, prompting the latest — and final — ruling.
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The school district got an anonymous phone call from someone claiming to have knowledge of the 2004 relationship.
The school conducted an investigation and fired Scipioni in October of 2014.
The Supreme Court’s decision will allow Scipioni to return to teaching for the first time since his firing three years ago, the Daily News reports.
Superintendent Philip Domencic issued a statement to the Daily News expressing his displeasure with the ruling.
The arbitrator found Scipioni at fault for his failure to be truthful to district officials and for a separate issue involving inappropriate emails, but noted the district did not accuse him of having an improper relationship with the student prior to her graduation, and he was not culpable for the relationship they had after she graduated.