An alien from planet Lorien (Alex Pettyfer
) was sent to Earth as a child alongside eight others to escape an invading race, the Mogadorians, which destroyed their home planet. He is protected by a Warrior/Guardian called Henri (Timothy Olyphant
) and has developed superpowers due to his extraterrestrial nature, such as enhanced strength, speed, agility, telekinesis, resistance to fire and heat, and the power to generate light from his hands.
The Mogadorians, led by the Commander (Kevin Durand
), know about the nine toddlers that came to Earth and search for them. The nine gifted Loriens can only be killed in numerical sequence, with three of them having already been slain. John is Number Four. Knowing this, he and Henri flee Florida to Paradise, Ohio, where John befriends conspiracy theorist Sam Goode (Callan McAuliffe
), a dog he names Bernie Kosar, and amateur photographer Sarah Hart (Dianna Agron
), whose ex-boyfriend, school athlete Mark James (Jake Abel
), is a bully who often torments Sam and now John.
During the spring carnival, Mark and his football cohorts accost John and Sarah, whom they believe are in a relationship, following them into the woods where they attempt to beat John up; however, John uses his powers to fend them off and rescue Sarah. Sam witnesses the events, and John, later confronted, reveals his true origin to him. Shortly thereafter, Mark's father, the local sheriff, interrogates Henri on John's whereabouts during his son and hospitalized friends' attack, noticing Henri's high-tech surveillance system.
With John's random displays of power (caused by his difficulty in controlling them) and too many people getting suspicious, Henri tells John they must move on, but John can't disappear just like that. He's fallen for Sarah in the Lorien mate-for-life kind of way.
As the Mogadorians close in on John, another Lorien alien, Number Six (Teresa Palmer
), hunts down the Mogadorians herself instead of running (a proactive decision after the murder of her Guardian). The Mogadorians eventually locate John and manipulate two conspiracy theorists into capturing Henri. When John and Sam go to rescue him, they are attacked but manage to fend the Mogadorians off. Henri is mortally wounded and dies after John and Sam escape with him and some Lorien artifacts, including a blue rock fragment that'll act as a tracking device to locate other Loriens. Sam's father, a conspiracy theorist who disappeared while hunting aliens in Mexico, had another. While Sam searches his home for it, John tries to say goodbye to Sarah at a party, only to discover that the Mogadorians have framed him and Henri for the murders of the conspiracy theorists, getting them additionally labeled as terrorists due to their suspicious use of cutting-edge technology. Mark sees John and calls his sheriff father, who corners John and Sarah. In saving Sarah from an accidental fall, John reveals his powers in the process. The two escape to their high school.
The Commander and his goon squad, having arrived in Paradise, block the exits with trucks. He confronts Mark and his father and, after injuring the latter, physically forces the former to show him where John is hiding, whereby Mark takes them to the school, knowing it's Sarah's usual hideout.
There, John, Sarah, and Sam are attacked by the Commander and his soldiers, who have brought two giant monsters to hunt down the trio. They are saved by the arrival of Number Six and John's "dog" Bernie Kosar, who reveals his true form as a good Chimera, which can shape-shift (sent by John's parents to protect him further). John, Bernie Kosar and Number Six (who can make herself invisible and block energy-based attacks) fight the Mogadorians. They eventually defeat them all, including the Commander, whose energy grenades are overheated by John and explode, destroying his body.
Bernie Kosar eventually shifts back into beagle form, bloodied and alive but favoring a very wounded paw.
On the following day, John, Number Six, Sam, and Bernie Kosar, the shape-shifting Chimera, unite their blue rocks and discover the location of the other four surviving Loriens. They set off to find and rally them together to protect Earth from the Mogadorians, leaving Sarah and a repentant Mark (who has redeemed himself by lying to his father about John's whereabouts and returned Henri's personal Lorien box to John) behind.