This betrayal really needs no introduction or explanation if you've played through the games. In essence its more of a reverse betrayal. It appeared on the surface that The Boss had defected to the Russians and launched a nuclear missile at a research facility. Its not until after you've killed The Boss do you realise that shed been loyal from the start and had defected under orders. The missile ending up being launched by a rogue Soviet general shows that in the end, The Boss had truly been innocent and only her death would prove the USs innocence.