Enslaved is a story set 150 years in the future where a global war has ravaged the Earth, destroying most of the human race and leaving the world to be plagued by robots left over from the war, known as "mechs". Although they are from a bygone era, they are still following their programming and seek to completely eradicate hostiles - in this case humanity.
The game opens with the main character, Monkey (Andy Serkis), awakening in a containment cell aboard a slave ship. He escapes and accidentally causes the vessel to crash. He manages to reach a woman named Trip (Lindsey Shaw) trying to leave the ship via escape pod, but she ejects the pod without allowing him to enter. When he regains consciousness after a fall, he discovers that she has placed a slave headband on him, which forces him to follow her orders and that if Trip dies, so does Monkey. Trip explains that she wants to return to her village, which is 300 miles away, and that she needs his help to get there. Monkey is angry, but complies when he realizes that he has no choice. The two travel across New York City toward the crash site, where Monkey hopes to recover his motorcycle. Along the way, glitches in the headband expose him to visions of what appears to be life before the war.
After visiting the crash site, the two travel the rest of the way on Monkey's motorcycle, but when they reach Trip's village, the place is deserted and overrun with mechs. After clearing the village of them, Monkey and Trip break into the safe room where they believe survivors are hiding, only to discover that Trip's father is dead and no other villagers can be found. Assuming everyone to be dead, Trip breaks her promise and refuses to remove Monkey's headband, explaining her intent to find and kill the person responsible.
Trip takes Monkey to meet up with a friend of her father's named Pigsy (Richard Ridings), who she believes can help them. Pigsy agrees to join them, and explains that a nearby mech base is currently housing an enormous and incredibly powerful weapon called the Leviathan. He gets a flying vehicle up and running, and the three follow a slave ship all the way to the base where the Leviathan is being held. They infiltrate the base, break the restraints off of the Leviathan, commandeer it and steer it in the direction of Pyramid, where the slaves are being held. Along the way, Trip apologizes to Monkey for breaking her deal and deactivates the headband, but Monkey tells her to turn it back on, hinting that they developed a romantic relationship on their journey together.
When the Leviathan reaches Pyramid, they are confronted with several giant scorpion-shaped mechs. The Leviathan's main cannon fends them off for a while, but one eventually climbs aboard and tears the cannon off, forcing Monkey to destroy the mech himself. With the Leviathan now defenseless and surrounded, Pigsy announces that the only way for them to destroy the opposing mechs is for him to overload the engines, which would blow up the Leviathan and kill Pigsy in the process. Trip frantically tries to convince him not to, but Pigsy demands that Monkey take her away from the blast radius, and Monkey complies. They make it away just in time to watch the Leviathan explode, bringing down all of Pyramid's mechs with it.
In the epilogue, Monkey and Trip enter Pyramid and discover that the slaves are under the control of a single individual. The man introduces himself as Pyramid (Andy Serkis) and explains that he lived before the war, and that he offers the slaves solace from the cruel world by sharing with them his memories of a happier era. He believes he is saving them, and pleads with Monkey and Trip not to take away what he has given them. Monkey recognizes the memories as the visions he'd been seeing with the headband on. Pyramid shows Monkey what he has given the slaves through a mask. Monkey becomes enthralled with the images, but Trip violently disconnects and kills Pyramid, shutting down the system and freeing the slaves. The scene ends with Trip asking Monkey if she did the right thing, leaving those in the pyramid and their future unknown.