Dead Space 
Prototype Story Comparison Both games tended to slowly feed you pieces of the plot as you went along. Overall, the plot of Dead Space was much more interesting than that of Prototype. Both have a twist in the end of course, but Dead Space wins on that one too.
The slow spoon-feeding of the plot in Prototype really broke up the story way too much because of the way it was delivered. They chose to use flashbacks to give you plot points, which take you out of the game entirely. Dead Space gave you story through audio and text logs throughout the ship, as well as conversations with other characters, which helped blend the game and the story together better.
If I had to compare the stories of these games to movies, I would say Dead Space is like Event Horizon + Alien maybe? Prototype is something along the lines of Outbreak + Bourne Identity.
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Dead Space is similar, since you arrive on the ship after everything went kablooey, but at least you have a significant goal in mind, which is gtfo. I dunno what I was actually trying to accomplish in Prototype.