SPOILERS!!!
This takes place in the year 2060 or so...
Sean Bean is Dr. Merrick, who heads an Institute built in an abandoned military facility in the Arizona desert. They sell cloning services to wealthy people for $5million, telling the clients that the clones (known as "products") are in a vegetative state, not conscious or truly human.
The reality is that the clones are grown from client's donated cells to mature adult development in 12 months, and receive memory implants of a real life, using variations of 12 different generic life memories. After their first 12 months developing in a large plastic sac, very roughly like the setup in the Matrix movies, the clones are then brought into the "world" which for them consists of life in an underground facility and being told that there was a "contamination" in the world and every once in a while a new person is found and decontaminated and brought to the place to live. This happens when a clone reaches their adult maturity. There is a daily lottery held for the clones, the winners of which get to move to "The Island", a fictional place where there is no contamination and life is perfect. The life of the clones is basically to bide their time waiting to win the lottery. The winners of the lottery are those that the clients need parts harvested from, and the clone is destroyed.
Ewan McGregor is Lincoln Six Echo (L6E here), a clone of Tom Lincoln (a wealthy single architect who designs fast boats, motorcycles, flying motorcycles, and the like) who has a lot more curiosity than the other clones, who have been designed not to question the status quo. He is friends with Jordan Two Delta (J2D here),(Scarlett Johansson), a clone of Sarah Jordan (famous model). L6E is also friends with McCord (Steve Buscemi) one of the "supervisors" of the facility (a technician employed by the Institute to care for the machines used to harvest the products). One day L6E has an opportunity to go behind the doors of the normal corridors, where he is allowed to go once in a great while, which he uses to talk with his friend McCord. While there this time he notices and capture a large flying moth, which shouldn't exist if they were all killed in the "contamination" and certainly couldn't get through the air filters that protect the colony from the outside polluted air. This piques his curiosity a lot more.
Dr. Merrick recognizes L6E isn't behaving as expected, and has the same nightmare each night, after a talk with him (Merrick is the resident counselor for the clones), and inserts little metal robots, the size of a large grains of salt which crawl into L6E's eye to record the brain activity.
L6E returns the moth to the back maintenance hallway and climbs up a long ladder to another level of the colony, which turns out to be the medical level where harvesting is done. There, with medical cloths put on to camouflage himself, he witnesses a lady giving birth and then being killed, the baby being given to the client who paid for a clone to bear a child for her. And then he witnesses another clone running and being brought down by guards after he escaped from an operating room table where they had started to harvest his liver. Mentally the clones come into the colony with the emotional and mental level of a toddler, and progress to illiterate 15 year olds.
J2D has won the lottery the day before, and this early morning L6E comes back to the colony with a glimpse of what's really going on, bursts into the womens wing and retrieves J2D and pulls her to come with him. By this time the guards are after them and they escape to the outside world, the arid Arizona desert outside the abandoned underground military facility.
Merrick hires ex military type to hunt them down and kill them, without letting the general public or police know what's going on. They make it to a small town, following a clue from a match box L6E had gotten from McCord. They arrive at the bar advertised on the match box, find McCord, and he takes them home and helps them get some normal street clothes and money and buys them train tickets to set them off to LA to find Tom Lincoln.
At the train station, hunters catch up with them, killing McCord. The train makes it to LA and L6E gets rid of the implanted robots which were being used to track him when he urinates. The hunters use the cities cameras which they've hacked into to locate the two clones as well as uses of the credit card. The hunters look for them at the departure station, but they sneak off and wander the streets. As the hunters go after them, L6E and J2D get arrested by the real police. Then the hunters ambush the police to prevent them from doing a DNA test, which would implicate the clients in the murder of McCord, which the real police think the two have murdered. The police are killed, but the two clones escape the police, hide overnight in some abandoned building. To this point they never kiss or are romantic with each other because of the conditioning they've received at the Institute. But now J2D is enjoying hugging L6E to stay warm.
The next day they make it to the home of Tom Lincoln, whose address came up on the police scanner while they were briefly in police custody and L6E was professing to be looking for Tom Lincoln. Using his identical fingerprints, L6E gets into the house, meets the real Tom Lincoln. Tom pretends to help them escape, take off their identifying bracelets from the Institute, but really sets up an ambush with the Institute's hunters. Big chase scene, lots of exciting action well shot, and it ends with Tom holding a gun on L6E, and they both profess to be the real Tom. L6E snaps the Institue's bracelet on Tom and the hunters then notice it and they shoot Tom.
L6E and J2D could escape to a far way land with Tom's wealth, but L6E wants to free the clones back home.
L6E now pretends to be Tom, and he's called back to the Institute to resubmit a DNA sample since the Institute is recalling the clones they've made for the past couple years (killing them) to correct a defect (independent thinking). J2D buys ice cream for children and uses the credit card, attracting the hunters and she gets taken to the Institute to have several organs harvested for the client who was in an accident and has 2 days to live. She manages to conceal a gun she took from Tom's house. L6E also has a gun.
So they're both back at the Institute, L6E to donate more DNA as Tom and J2D to be harvested and killed. J2D shoots the guard and escapes the operating room dressed in medical garb, L6E escapes his Institute guide, they meet up and we see they planned for J2D to get grabbed and brought back.
The head hunter (Laurent - played by Djimon Hounsou) realizes that his customer, Dr. Merrick, really is evil, and that J2D was brought back to be killed for her organs but that the client is too far gone to be helped, but for the money she was going to get the clone's organs anyways. Laurant then goes and helps J2D free the clones in the process of being gassed to death, while L6E fights his way to sabotage the hologram generating device that surrounds the colony with an image of an outside world that doesn't exist, with an Island in the background.
L6E fights Merrick himself, destroys the huge fan that draws in fresh air for the underground facility, causing the huge blades to whirl around and down destroying the hologram machinery and opening a way of escape to the real outside world of Arizona desert.
