Former Luton Town boss Nathan has retuned to Kenilworth Road as the club's new manager.
Luton were second in League One at the time, and went on to win the division, while Stoke were in the Championship.
Jones described the decision to leave as the "toughest of his life" but admitted he couldn't turn Stoke down.
However, Jones went on to endure a torrid spell at the bet365 Stadium and was sacked in November last year with the club in the Championship relegation zone.
Jones famously angered Luton fans in January 2019 when he was pictured receiving the League One Manager of the Month award in his new Stoke kit - despite winning the award for his final month in charge of Luton.
The Welshman will now be hoping to win supporters back over though after agreeing to replace his namesake Graeme Jones who left Luton by mutual consent in April.
Nathan Jones led the Hatters to promotion from League Two as runners-up in 2018 and won 87 of his 170 matches in his first spell in charge of the club.
Jones takes over a Luton team who were second from bottom in the Championship and six points adrift of safety before football was suspended in March.
Chief Executive Gary Sweet said Jones' knowledge of the club would give the Hatters the best chance of survival.
“We must do everything we possibly can to stay in the Championship this season. We have just nine games left to climb out of the relegation zone and the squad has to be more than ready," said Sweet.
“We need a manager who can hit the ground sprinting – someone who knows us, our players and our environment and someone who knows the league.
“There’s only one man who has those characteristics and that’s Nathan Jones. And there’s only one person who should be assisting him at this time – and that’s Mick Harford.
“Everyone knows exactly what we thought about Nathan when he left for Stoke – we hardly made our disappointment a secret.
“For the sake of the club, all I ask of supporters is to give him time but also to get behind everyone for these nine games.”
Hear Nathan Jones on his regret in the way he left Luton, on 'that photograph' at Stoke, and Luton's CEO Gary Sweet on why they've re-appointed him, speaking at their Zoom video news conference