Flawed but fun
I am so confused by this trilogy's plot. How can he kill her if she's taken the immortality potion? Why is there a card renewal machine in a prison cell? The Bible stuff seemed shoehorned in, too - I think it would have been cool if the passages displayed gave a hint for a puzzle or something, so that they had relevence.
I loved some of the puzzles, though - especially the one at the beginning with the sink and the mat and so forth. The last room was really frustrating, though. I enjoyed the heck out of the shooting part, even though it took me a couple tries to beat.
The animation has a lot of rough edges, but for one person making an independent flash game it's really impressive, and the work you've put into the visuals pays off - kudos on that.
Overall, the plot reached a Matrix Reloaded level of confusing and the puzzles ranged between fun and annoying, but overall I enjoyed it.