Now, Jones is apparently gone for good.
During Wednesday's practice, O'Brien told a group of reporters that Jones was no longer a part of the Penn State football team due to personal reasons. He did not answer questions nor provide further details.
So it remains unclear if Jones quit the team again -- as had been rumored late Tuesday night and throughout the day Wednesday -- or if he had been sent packing. Or, for that matter, if it was some combination of the two.
Regardless, a Penn State career that began with promise is now over. Jones was a Scout.com five-star quarterback recruit who graduated early from high school so he could enroll at Penn State in January of 2010.
He was a standout in the spring game that year, throwing a pair of touchdown passes. Jones took a redshirt in 2010 and then missed the entire 2011 season due to academic issues.
He was back in good academic standing in the spring and finished second in the Nittany Lions' three-man quarterback race -- behind Matt McGloin and ahead of Rob Bolden (who would later transfer to LSU).
But earlier this season, Jones was passed on the depth chart by true freshman Steven Bench. O'Brien asked the 6-foot-3, 258-pounder to move to tight end for a Week 2 road game at Virginia.
That is when he first quit the team.
I wasn't thinking about the whole big picture and everything, Jones said a week and a half later. I didn't want to play the position at all. Actually, I quit for about 20 minutes. Then I just thought about everything me and Coach O'Brien talked about. I really didn't have anything to lose by trying this new position, so I figured I might as well go at it with an open mind and try it out.
Jones did not play against Virginia. But the following week, in a home win over Navy, he caught one pass for seven yards and a first down. In last weekend's win over Temple, Jones had one carry for a seven-yard loss and did not catch a pass.
Earlier Wednesday, as word spread that Jones missed Tuesday's practice and was not longer with the team, McGloin responded.
I'm very good friends with Paul, McGloin said. We have great relationship. It was a shock that I heard that he wasn't gong to be around anymore He's the type of kid who wants to contribute any way he can, whether it be at tight end or quarterback. I was really upset that he made the decision. But at the same time, he has to do what's best for him.
It is not clear if Jones will remain enrolled at Penn State. Since he played in two games this year, he is not eligible to transfer to another school and play immediately. Due to NCAA sanctions against PSU, he can transfer after the season and be eligible to play at the new school in 2013. He will have only two seasons of eligibility left if and when he transfers.
Jones was spotted in at least one class Wednesday, wearing a Penn State football warmup suit.
Jones is the second Nittany Lion to leave the team during the season. Prior to the Navy game, receiver Shawney Kersey also left for what O'Brien described as personal reasons.