Jones had offers from
Rutgers,
DePaul,
Marquette and
St. Johns before settling on Syracuse.
2008–09 Jones would make his debut against
Le Moyne, playing 10 minutes and scoring three points. The freshman would make his biggest impact in an 86–51 win against
Colgate on December 1, 2008, as he played 21 minutes and scored nine points. On January 26, 2009, it was announced that Jones had suffered a muscle tear in his right hip and would miss the remainder of the season. He received a medical redshirt.
2009–10 During the November 24, 2009 game against Cornell
Jim Boeheim approached Jones and had words with him. Mookie then got up and flung his headband as he disappeared into the tunnel leading to the locker room. Jones reappeared with 90 seconds left in the game to shake hands with Cornell. When reporters were allowed in the Syracuse locker room Jones was not at his locker. Jones cleared things up with Boeheim following the game and would go on to score 12 points in just 14 minutes the following game in an 85–60 win over
Columbia.
2011–12 In 2012 Theodore (Mookie) Jones decided he was "done playing for Syracuse" after he was suspended by the university for a year after being accused of cyberbullying in the fall of 2011. The suspension would put Jones’ eligibility as a student-athlete in jeopardy. Jones left the team and university in the winter of 2012. After returning to college later, he graduated in 2015. ==After college==