Question: “although Johnson realized what was going on, he played his allotted part” question.

[ahln1239]

President Johnson knew the purpose of the S3 Program but he still did what the Patriots intended for him to do rather than fight against it.

It's worth noting that this is potentially only Ocelot's idea of the S3 Program, the Solid Snake Simulation, in which Johnson is a stand in for Baker-who dies but not before imparting the knowledge on how to stop the nuclear launch.

thanks so much!

i would like to ask you this as well friend, if i may:

wiki:
"The worm was uploaded into GW during the Big Shell Incident, though its progress was seemingly halted at 90% by an antibody agent. Despite this, following a slight delay, it eventually began to affect GW. Raiden discovered this when his supposed C.O., the Colonel, began to act in a strange manner and was revealed to be an AI construct of GW's. The worm then fully corrupted the GW system as well as everything connected to it, with Revolver Ocelot informing Solidus Snake of this just as the corrupted RAYs were starting to go haywire, also forcing the Arsenal Gear to surface...." 
"in addition, one of the AIs when contacting Raiden nearing the end of the mission implied that the worm, while crippling GW, nonetheless managed to perfect the AI in the process largely because of the S3 Plan."

now i really am trying my hardest to understand two things:
1. why the patriots wanted the virus to stop at 90, what was the plan? why the delay (the delay was until the virus was complete after a while when the rays went haywire.)
2. why it perfected the gw? the worm cluster i mean...? was it due to the pressure it was handling all at once? (the virus)
then again, i thought the patriots don't care for gw's ai, only the s3 plan no? so why they wanted to perfect it?

thanks a lot friend, you are a lifesaver for sure