You are enlisted by S.A.A.T to help them find out what sank the Virago. You must decode the data log, send the information to F.A.T.H.E.R. then deal with the Virus and help find the origin. After F.A.T.H.E.R. runs a scan, he gets infected then you have to deliver the Anti Virus. After the Anti Virus is administered, F.A.T.H.E.R. loses control of C.O.R.E. then disconnects his Ark from the emergency braces and needs to be dealt with using help from the Eden Initiative and Global Trust Inc. once you convince them.
Run a diagnostic on the data log through a chain of researches from the Tech lab.
First, you must choose to settle on (work with) an Eco or Tycoon island. If you settle on one, you get a diplomacy boost for that faction but you can get a diplomacy and influence bonus (and a special item that prevents dissatisfaction--this comes in handy later) if you click on the warehouse of the other island and complete the mission the manager gives to you. Build up your population as much as possible but try to ascend as many workers as possible as well because you want residences to be able to feed off advanced food when the fish supply goes out.
F.A.T.H.E.R. runs a complete analysis of the data log and discovers that the problem was an intelligent virus, he gets corrupted by it and puts C.O.R.E. in danger. At the same time, the virus makes your fisheries produce rotten fish. Set up a trade route (if you have not already) to import functional food and rice or super spice to feed your lab assistants and employees. Dr. Bartok is deemed an enemy by F.A.T.H.E.R. and sets up a warehouse on the edge of the C.O.R.E. island. She will give you a special data log to help you create an Anti Virus and a mission to fix your fisheries. F.A.T.H.E.R. will attack your ships and destroy your data log if you get caught before you can unload your data log into your warehouse.
The computer virus from the sunken Ark Virago has infected F.A.T.H.E.R.'s systems. The super AI disabled C.O.R.E. by disconnecting his Ark from the safety restraints then submerged. Without energy, and stricken with a series of incidents the City can barely function.
Professor Devi has asked representatives from Global Trust Inc and the Eden Initiative to come to the scene of the events. While Rufus Thorne and Yana Rodriguez are quite happy to provide help with rebuilding C.O.R.E. they are quite sceptical of the threat posed by F.A.T.H.E.R. and so you must provide evidence to Rufus and Yana showing that the rogue AI is a serious threat.