Your writing is very readable. The punctuation is great and I didn't find any errors.
The main characters were interesting although a little more development would be a plus.
Your plot has lots of potential but the story lines don't tie in as well as I'd like. Dr. Tjener's work, for example, we know it exposed the lack of free will and led to the Conclusion, but what did it have to do with John's activation? It just seems to me that Dr. Tjener's work doesn't lend enough substance to the over-all plot climax.
This is also somewhat true with Hope. I think there needs to be more of a tie in to the climax of the plot for her. When the characters are introduced and interacted with, then not tied solidly into the plot, they run the risk of becoming viewed simply as "filler" between the beginning and end of the story. Now, if maybe Hope had not shown for a date and went missing in the days before John's activation, and John investigated this finding hints that she had been activated already, this would tie her into the plot stronger (in addition to being a great opportunity for adding suspense in the form of mystery).
One last critique, as if I haven't slammed it enough already, I'm sure you know that all stories have a beginning, a middle, and an end. For a short, your beginning is very nice, the middle is OK but bogs down slightly, and the end is kinda abrupt. Not in the sense that John discovers his activation right at the end; what I mean is it goes right from the middle to the end with little segue except for John's stomach cramps.
Please don't take my criticism the wrong way or let it discourage any at all. Like I said to begin with, your writing is great and your story has lots of potential. The only writing I have done in college courses was non-fiction so my critique is strictly amature.