quick question about mgs 2(SPOILERS)

ok so you know how towards the end roy cambell says hes a computer program and not human and they say none of the stuff raiden did on the shell was real. was it real or not? someone explain it to me

The stuff on the shell was real. Its the mission was false as well as the ransome and the hostage being shot on the roof

The "Colonel" was just an AI program created by the Arsenal Gear that pretended to be Colonel Campbell inside Raiden's nanomachines. In other words, Raiden was just talking to himself when he thought he was talking to Colonel Campbell. The reason why the Colonel started acting weird was because Emma Emmerich uploaded a virus to the Arsenal Gear which affected the system and the AI program that was talking to Raiden.

I know it's really confusing at first, I mean I had to play through the game a couple times to fully understand it :P