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I have completed the game once, and I'm towards the end of my second run through the game, but I seem to be stuck. There are no missions available, and no way for me to get back to the prison to continue the story and complete it again.

I am not sure how to proceed from here. Will someone be able to help me?

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What was your most recently completed (main, non-sidequest) story mission? –  Christopher Berman Jul 25 '12 at 23:16
    
I was playing through the story normally and 'helping the Scientists' in the lab. But i have no flags or '!' to go to for missions. I have been round back to all areas (jungle, slums.. etc) in case i had missed something but no –  stuart Jul 26 '12 at 8:18
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2 Answers

When you load the save or reload a checkpoint, you will be inside the laboratory, facing the door to Dr. West's office, go inside the office and open the small fridge opposite the door and take the antidote. After that you will need to interact with the radio on the table to go to prison (don't pass go).

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My theory is that you accidentally fast travelled out of the prison by loading last checkpoint while highlighting a mission not in the prison. However, I would've expected you to return to the prison the next time that you load up the save file from the title menu.

If you've already been to the prison on that playthrough, fast travel maps will allow you to fast travel to the prison. kotekzot's theory that you haven't retrieved the antidote sounds slightly plausible too. In any case, you can click play at the title menu, new game, pick the same character, choose the chapter closest to your progress, which sounds like chapter 16 which is the start of the prison, as desireable, and select your old character's data to play with. Don't worry, this creates a copy of the save file.

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