The Anomaly starts with Ryan Reeve waking up in the back of a van with a young boy chained up. He frees the boy, and when the van stops at a light, they jump out of the back and run off. While hiding from the guys in the van, Ryan reveals that he was a soldier undergoing treatment at a facility, but that was some six months ago. He doesn’t remember anything since then. The boy says that these guys in hoods broke into his house and kidnapped him. Ryan then finds one of the hoods in his coat.
The movie is a series of scenes where Ryan wakes up not knowing what has happened since the last time he was awake. It turns out, that the doctor treating him has invented this thing that lets him take over the body of someone else. The doctor is dying of some disease, but he can work on his plan with another body. The reason Ryan keeps waking up, is that there are solar storms that interfere with the satellite signal used to control the body, and it takes the system some nine minutes to reboot. So Ryan has nine minutes at random times to try to take his body back.
The doctor and his son work to free a genetic engineering terrorist to create a version of the technology so that instead of surgically implanting it, they can just infect people with it. And the boy is this terrorist’s son, kidnapped so the father would work with them.
There are subplots with the CIA, these Russian brothel owners, and a prostitute that Ryan befriends. In the end, the bad guys are stopped, and it looks as if Ryan and the prostitute will adopt the boy.