The story was to proceed with the protagonist being sent on a few tasks by Dr. Caldwell. Meeting Caldwell's colleges. And eventually being sent to retrieve something from the other group of former Rapture inhabitants, being led by Caldwell's wife and former best friend, who both "betrayed" him. This group was to have continued down the same road of plasmid abuse that was seen in Rapture, using it for fun, pleasure, and as weapons. They were also going to display the kind of desperate junkie desire/need for ADAM that was seen by the splicers. This group won over the native islanders by demonstrating their ability to use "magic" and now have essentially a whole army at their disposal, some of which have been taught how to use plasmids themselves. I figured as the story went on, this group might start to display signs of being "spliced up".
From them Reid would be introduced to plasmids and begin using them himself, and learn that Dr. Caldwell hadn't been entirely honest with him about everything. He'd find himself caught in the middle of a power struggle between the two groups of former Rapture scientist, uncovering the mysteries of what was going on, and trying to figure out which group was more trustworthy, or the lesser of two evils.
That is really as far into the story as I ever mapped out. I ran out of ideas, and realized I was wasting my time on what was simply fanfiction, something I've never been too fond of, my heart wasn't in it, my writing was sucking, and I just kind of dropped it.