The centre-back, 27, returned on a free transfer from Watford a season after leaving the Iron for Vicarage Road in a Bosman switch.
He proved surplus to requirements at the Hornets last season, making just four appearances before returning to Glanford Park on loan.
He featured 19 times and was instrumental in helping steer the club away from the relegation zone.
He has signed a two-year contract, and is likely to be partnered with Paul Reid as the Iron's first-choice centre pairing.