The 21-year-old handed in a transfer request to manager Adam Murray after expressing a desire to move closer to his native North-East.
Thomas linked up with the Stags in the summer of 2015 and has made 21 appearances for the club this season, 12 of which were as a substitute, scoring one goal in the 4-0 win over Crawley Town in September.
Murray said: “Nathan came to us last week with a transfer request.
“This has been one of the toughest calls I’ve had to make as a manager because I was close to Nathan as a person.
“He’s only ‘a baby’ and has been around the country trying to settle and plant some roots for him and his family.
“An opportunity came up for Nathan where he has the chance of a longer contract – a bit more security – and it takes him back home.
“For him and his family it was one he couldn’t turn down, so his agent asked us, for personal reasons, would we allow him to go back home?
“I have let him go with a heavy heart as I think in spells, he has shown that he is a good player. The thing with Nathan was we needed consistency from him on the football pitch.
“For 10 minutes here and 20 minutes there he was brilliant, but we needed to be able to rely on him to start games week in week out, and in my eyes, he wasn’t at that stage of his development. “Nathan wants to play every week as well, which is understandable. “Hartlepool came in for him and we’ve come to an arrangement which suits both parties.”
Murray added: “Nathan’s representative asked me at the time if we were able to commit to Nathan’s future past this season. If I am being totally honest and protecting the football club, in my eyes, Nathan hasn’t quite done enough to warrant that yet.
“Everyone is fighting to be part of this journey and it’s a tough fight.
“The big thing with him for me is that he has gone from Newcastle to Sunderland, then down to Plymouth and up to Motherwell - he has been chasing some settled ground.
“I couldn’t turn down his chance of going home where he can get back with his family and play his football, hopefully play on a regular basis.
“I couldn’t stop that opportunity if there was a chance in four or five months I’d been telling him he hasn’t got a job, that wouldn’t be fair.
“Nathan reminds me a lot of myself probably 10 years ago.
“He is a fiery character and he needs some foundations in his life, and for me to keep him here with the risk he could be in the rat race at the end of the season, I couldn’t do that to him as a person.”
Thomas tweeted: “I am delighted to announce that I have signed for Hartlepool and I am looking forward to a new challenge and getting the club back up the league
“I would also like to thank Adam Murray and Mansfield Town for the chance to play for them and wish the clubs, players and fans the best of luck for the future and their promotion challenge.”