Just about lost interest at this point. So the military decide to take action against the human compound and retrieve the mysterious weapon that is destroying the surrogates, and their human controllers. Meanwhile, a surrogate breaks into the home of Peters and kills her - then takes control of her surrogate as well.
Just before the compound is attacked, 'The Prophet' orders that the weapon be taken to Peters ... before the GI Joes arrive and shoot a few protestors - including The Prophet, who turns out to be just another surrogate ... controlled by old man Canter. You'd have thought his friends would have seen that one coming - especially as old man Canter would need to make the odd bathroom break every hour or so.
Peters tricks Greer to help her retrieve info from the FBI database - and he shoots Stone's surrogate to break into his office computer. Peters soon turns on him and escapes with the weapon. She heads to the FBI HQ, where she holds hostage the nerdy guy who monitors the surrogates and begins to hook up the weapon to the mainframe.
Stone enters the FBI offices, and admits that he was behind the assassination of Canter's son - thinking it was Canter. Canter, who is controlling Peters, shoots him dead without remorse. Greer is at Canter's home and breaks his way into the inner office. Canter admits that he regrets ever creating his big invention, and wants humans to return to their own lives. He shoots himself.
Greer quickly takes control of Peters, and just in time puts up some type of firewall to protect the humans from having their brains fried. He then has the option to disable the weapon - but instead decides to destroy all the surrogates all over the world.
Instantly all the surrogates drop dead. The world is quiet. People slowly venture from their houses and shake hands with their neighbours.
Greer returns home and kicks the door down to his wife's room -- but she is already outside, sitting in their son's bedroom. They hug and Greer is relieved to have his wife back ... even though she has a noticeable Vitamin D deficiency. And fangs.