The year is 2023, a gruesome disease has broken out in the Manhattan Island, New York City.

You are sent to extract Dr. Gould to have his help with the alien invasion. They send in Alcatraz (that's you)  and his team (you are part of the Marine Force Recon Unit) you all are on a submarine to get a person named Dr. Nathan Gould. He was once part of the crynet job who had important information about the Ceph and how to stop them because he has studied them for years inside the offices at C.E.L.L Headquarters (they are the Lockhart and Hargrave forces)  to see how they work. How they are made up. What they were made to do. Later he found out that they are made up of nanites when he still worked for them before so he knows a lot about them and he also knows about C.E.L.L and what they do. While at one point being a  biological researcher to study them there, so you are sent to go get him to help in the fight against the Ceph because Hargreave dropped a nuke on an island that the Alpha and many others on and it gave them enough energy to reawaken. (They've been on earth for 65 million years and they have laid dormant for most of the time only waking when something major happened until the alpha was woken up and then the alpha woke the others because the alpha woke the others up and started to control them through their mind.) But things go south quickly when the ceph attacked and you lost your people and almost yourself but you made it out alive but also because of that you are the last one alive but you have heart, lung, back and sternum trauma. But there is also ruptures in his lungs, multiple broken ribs, and a condition where your ribs are broken and they get detached from the chest wall which means your ribs are going into your lungs.

Which later get healed by the Nanosuit given to you by the real Prophet because he thought he had gotten the Manhattan virus which kills the host. Instead, he gave you the Nanosuit so that you would have a second chance at life but you take his place as "The Prophet" and you take his place and Dr. Gould contacted you who he thought was Prophet, no one knew that he gave you the suit. Then Gould told you to come and get him so you two can figure something out and you had to start fighting through all the guys who are thrown at you by Commander Dominic Lockhart and Jacob Hargreave. Because they still don't know that you aren’t Prophet.

Once you are done fighting them you start  and you find Dr. Gould, he hooks you up to a device that is like a chair but it leans back (it's stuck in that position) that hooks into the back of the suit and then that shows the insides and what the person has seen because of the suit and how it records everything you do and see, He then sees that you aren't the real Prophet and how you for the suit and "filled in" for him and started listening to Dr. Gould without saying anything but when he saw that you weren't who he thought was he tried attacking you but you guys started working together despite that and it was also still your mission to get him out of his safe house but his safe house was compromised and you have to fight your way out. As you are fighting your way out you are captured by the commander and taken to a place where he wants to get the suit from you but you break out.