Even though I know it may be a stretch, they could in fact manage to pull out a new show based on John Doe. We know he has no memory, we also know it's because of some sort of gov't coverup. He's currently on Prison Break as a death row inmate. What if Scoffield's ultimate plan to save his brother was to give him a pill that would make him appear to be dead but also allow him to survive the electric chair (sabotage the chair to not really deliver a lethal dose of electricity but since he appears dead it isn't caught). After he is executed and his body is sent off for burial, he's revived by a 3rd party and dumped in the woods thus beginning the series John Doe. Scoffield was supposed to pick him up, but somehow either he got sidetracked or the people delivering John Doe had to dump him randomly to avoid being detected. His memory loss could be a side effect of the pill and the death experience.
This would allow both Prison Break and John Doe to continue as either sister series or be merged back into one (Prison Break being the prequel to John Doe). The cool part is that you'd have to end this season of Prison Break with my above scenario. The 2nd season of Prison Break would be Scoffield on the outside trying to find his brother and instead find more details about the conspiracy involving his brother and another group that wants him to stay alive. There would be near misses between the two brothers in every other episode (passing eachother on opposite sides of the street or even being in the same building at times). John could even see Scoffield off in the distance, but just doesn't remember him. You end this season to line up in conjunction with the events at the end of the 1st season of John Doe, but with the two brothers meeting face to face for the first time since Prison Break.
The NEW season of John Doe would have the two brothers talking and Scoffield trying to fill John in on the details that he's missing. It would be a mission for both of them to try to recover John's memories and to find his son. With John having all that knowledge and Scoffield's pattern recognition abilities, you could squeak out a good season if there's good writers onboard.
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Even though I know it may be a stretch, they could in fact manage to pull out a new show based on John Doe. We know he has no memory, we also know it's because of some sort of gov't coverup. He's currently on Prison Break as a death row inmate. What if Scoffield's ultimate plan to save his brother was to give him a pill that would make him appear to be dead but also allow him to survive the electric chair (sabotage the chair to not really deliver a lethal dose of electricity but since he appears dead it isn't caught). After he is executed and his body is sent off for burial, he's revived by a 3rd party and dumped in the woods thus beginning the series John Doe. Scoffield was supposed to pick him up, but somehow either he got sidetracked or the people delivering John Doe had to dump him randomly to avoid being detected. His memory loss could be a side effect of the pill and the death experience. This would allow both Prison Break and John Doe to continue as either sister series or be merged back into one (Prison Break being the prequel to John Doe). The cool part is that you'd have to end this season of Prison Break with my above scenario. The 2nd season of Prison Break would be Scoffield on the outside trying to find his brother and instead find more details about the conspiracy involving his brother and another group that wants him to stay alive. There would be near misses between the two brothers in every other episode (passing eachother on opposite sides of the street or even being in the same building at times). John could even see Scoffield off in the distance, but just doesn't remember him. You end this season to line up in conjunction with the events at the end of the 1st season of John Doe, but with the two brothers meeting face to face for the first time since Prison Break. The NEW season of John Doe would have the two brothers talking and Scoffield trying to fill John in on the details that he's missing. It would be a mission for both of them to try to recover John's memories and to find his son. With John having all that knowledge and Scoffield's pattern recognition abilities, you could squeak out a good season if there's good writers onboard.