Question: Why the patriots did these things? hard questions.

[Dirty Duck]

Have you finished the game yet? I think it will give you a satisfactory answer to these questions, if you're still wondering afterwards though:

MGS2 spoilers:

It was all a carefully curated plan to test how The Patriots can control the narrative in the Information Age and control people's actions by dictating what context is created around events. The part of GW affected by the virus is not the entire system, but instead a partition of the system that was being used as part of the S3 program. It, and Arsenal Gear, isn't actually important to The Patriots. Both were theatrics to see how they could control the outcome of the events. It was all staged. The entire thing was essentially a testing ground for aspects of The Patriots plans that were more important than anything going on in the Big Shell.