In a pine forest on a small island in British Columbia, Canada, (which is nothing like the tropical islands from the "Far Cry" video game), a group of armed mercenaries is savagely obliterated by an unknown foe. Evil mastermind Dr. Krieger observes the brutalities with obvious pleasure from CCTV cameras.
We cut to Jack Carver, the German ex-special forces soldier turned boatman and the movie's protagonist, sipping from a beer can and driving his boat, while his passengers request him to show them whales in the Canadian lake. He dismisses their whale request and leaves them disappointed.
Dr. Krieger, the evil mastermind, reveals that his latest genetically modified (and mindless savage) super-soldier is a great success, capable of eliminating more than ten armed soldiers. The commander of the island's armed forces, Jason Parker, protests against using humans as "target practice", but Dr. Krieger convinces him not to care, for the victims have not been his men, but mercenaries led by his right-hand woman, the sadist Katia Chernov.
We cut to a newspaper office, again somewhere in Canada, where young reporter Valerie Cardinal (and not Valerie Constantine, as she is in the video game) decides to go on a solo mission to investigate Dr. Krieger's top-secret island facility, despite her chief's protests. She is a journalist and not an undercover C.I.A. agent, yet another deviation from the game's storyline. we understand that her Uncle Max works there, though it is not specified what work exactly he's doing, and that he has been feeding her information. We'd previously seen Max agreeing with Parker about how bad it is to use men as test subjects.
Val hires Jack Carver to take her to the island, because her uncle Max has set a meeting up. Turns out that Uncle Max and Jack have served together in the army and have known each other for a long time. However, Uncle Max is captured by the evil mercenaries while trying to send Val an e-mail with more information, and is put to the same surgical "genetic" enhancements that the other mad super-soldiers have been put through, because the government has decided to shut the funding as the project is becoming more dangerous. Dr. Krieger hopes that Enhanced Uncle Max will be obedient and will help him get his cash back. (Note: The super-soldiers look nothing like "Far Cry's Trigens, by the way, and are simply people painted light blue, with no primate or "fat boy" varieties.)
Jack and Val reach the island and Val goes off to meet her uncle whom she thinks awaits her, but she's ambushed by the evil mercenaries who are awaiting her instead of her uncle. Jack's boat is destroyed and he nearly gets away from the explosion, managing to save Val in the process. With our heroes hunted by the mercenaries, a long car chase ensues, until finally Jack's car is airlifted by a helicopter (don't ask) and dropped into a lake, with the helicopter exploding (once again, don't ask). Jack and Val, having slipped their foes, find their way to an abandoned house where they get out of their wet clothes and, due to the cold night, share body heat (If the film took place on tropical islands as it should have, they wouldn't have had this problem...) in more ways than one. On the next morning, Val, upon Jack's inquiry, gives him two points "from the scale of one to ten" about his performance in the heat-sharing activities. This unexpectedly low rating seems to be more important to Jack than anything else that happens afterwards.
Jack is determined to take a boat and get off the island, Val insists they get Uncle Max first - she doesn't know he's been "enhanced". They manage to infiltrate the bad people's HQ and Jack leaves Val to hide while he finds a boat. Val, however, hides in such a way that she is perfectly observable from a CCTV camera and soon enough, the mercenaries come and capture her as well. Dr. Krieger, ever the gentleman, gives her a tour of his facilities and shows her her enhanced Uncle Max. Uncle Max, however, is currently sedated and does not react at the sight of his niece.
Meanwhile, Jack finds a food-laden boat along with its whiny captain, Emillio "The Food Guy", who should not have even existed. Due to a misunderstanding or two, Jack briefly meets Parker the good soldier, and then knocks him out, and kidnaps the boat along with Emilio (who doesn't stop yelling in the most annoying way imaginable). After a considerably long boat chase, Jack and Emillio are finally stopped, captured and taken together, Emillio considered his accomplice. Dr. Krieger presents Jack to Val, (which gives her a chance to give him a key for his handcuffs), and then lets Uncle Max out and orders him to kill Jack. Jack manages to show him Val, and Max decides he isn't as bad as the rest of the "enhanced" soldiers and helps Jack defeat the other bad guys that Krieger turns on them. This results in Krieger releasing all of his mindless super-soldiers, who start murdering everyone. Krieger attempts to escape, but Parker, the good soldier, opposes his "hold the line 'till death" commands and orders his men (the soldiers) to evacuate first. Krieger however turns to Chernov(a)'s mercs and commands them to kill the soldiers and to escort him to his boat, along with Val who is still a hostage. After a long firefight and a "we're on the same side" talk between Parker and Jack, Parker gets killed by the evil Chernov(a) and his soldiers are decimated. The rest of the enhanced mutants take care of the mercenaries however, and Uncle Max saves Val and kills Chernov(a), though sacrificing himself. Jack is wounded in the process, and it seems that there are no more boats left to leave on, and the last of the mutants are getting closer. In that precise moment of desperation, Emillio, who had ran off sometime before, appears and saves the good guys while leaving Krieger to his doom.
In the final scene, Jack and Val are talking on the pier. Val complains that the government has prohibited her story as a breach of national security. Jack shows her his new boat, which now features Emillio as the cook. Val leaves for work, promising that she'll return the next day, leaving Jack to conclude that his one-to-ten rating of two wasn't real. His day isn't left unspoiled, however, because his new boat's first passengers are the annoying whale-loving couple from the beginning of the film, come back to verbally torture him. In the final shot, Jack walks away and leaves Emillio to do the cruise himself.