A game designer on the run from assassins must play her latest virtual reality creation with a marketing trainee to determine if the game has been damaged.
Allegra Geller, the leading game designer in the world, is testing her new virtual reality game, eXistenZ with a focus group. As they begin, she is attacked by a fanatic assassin employing a bizarre organic gun. She flees with a young marketing trainee, Ted Pikul, who is suddenly assigned as her bodyguard. Unfortunately, her pod, an organic gaming device that contains the only copy of the eXistenZ game program, is damaged. To inspect it, she talks Ted into accepting a gameport in his own body so he can play the game with her. The events leading up to this, and the resulting game lead the pair on a strange adventure where reality and their actions are impossible to determine from either their own or the game's perspective.
- At a Antenna Company seminar, Allegra Geller (Jennifer Jason Leigh) is introduced as the "goddess of the gamepod". She carries a single ski boot and describes eXistenZ, which is a new game system (metaflesh). Almost everyone in the room volunteers to test the new system. At the door, a game company worker Ted (Jude Law) screens Noel Dichter (Kris Lemche) for recording devices. Noel has an outdated gamepod, and is anxious about the demo.
The demo uses flesh like gamepods to allows players to interact with the game. As they go into a trance to enter the game, Noel pulls an odd-looking gun out from inside his gamepod and shoots Allegra in the shoulder. The gamers attached to her feel the impact, and Noel gets shot by security. Ted grabs the gun and whisks Allegra away. In the car, Allegra throws Ted's phone away, as it can be used to track them. He uses a pocketknife to dig out the bullet, which is a tooth. They realize the gun and ammo are made of flesh and bone, which would not be detected by a scanner.
They stop at a motel. Ted wants to check in with Antenna, but Allegra wants to test the game, and needs Ted to help her. Ted does not have a "bio-port". They go to a gas station and ask the attendant Gas (Willem Dafoe) to install an illegal port. He agrees, after recognizing Allegra. When she connects her pod to Ted, it short circuits, locking everyone out of the game. Gas reappears, holding a shotgun, and explains that Ted's port is useless. Ted shoots Gas in the neck before he can kill Allegra.
Allegra and Ted drive to an old ski club, where they find Kiri Vinokur (Iam Holm). She hands the ski boot to Kiri for safekeeping, then Kiri and Landry (James Kirchner) work to repair the pod. Afterwards, Allegra and Ted jack into the game, and Ted's reality changes. Allegra says "you have to play the game, to find out WHY you're playing the game. They meet a gameshop owner, D'Arcy Nader (Robert A. Silverman), and Ted realizes the non-player characters (NPCs) must act based on his actions and speech. Nader gives them micro-pods, and they use them to port in. Ted's character makes a pass at Allegra, and she responds.
During the encounter, the scene suddenly changes, and Ted is at a trout farm, working on a conveyor belt as "Larry", next to Yevgeny Nourish (Don McKellar). Yevgeny explains that the trout farm is now used for making game pods. Yevgeny recommends lunch at the Chinese restaurant, and to order the special. He finds Allegra, but she seems to react like the NPCs as well. Over lunch, Ted tells her he is nervous, and manages to pause the game. Back in reality, Ted starts to feel like the real world is fake, and vice-versa.
They re-enter the game, and special of the day arrives. It's gross looking, but Ted's character eats it anyway. He assembles the bones into the same weapon that he found in the real world. He shoots the waiter (against his will), and the weapon is destroyed. Yevgeny appears, and tells them the waiter was a traitor. Yevgeny leads them to a breeding pool for the creatures and explains that they are working on undetectable weapons for a secret agency in addition to pods. The trout farm where Ted and Allegra work is owned by a company called Corticle Systematics, and Yevgeny's organization wants to destroy all non-real elements such as pod games.
They return to the gameshop and speak with Hugo Carlaw (Callum Keith Rennie). Hugo shows them Nader's dead body and tells them Nader and Yevgency Nourish work for Corticle Systematics, and Ted shouldn't have killed the waiter. Hugo is with the realist underground. He tells them to assassinate Yevgeny. They return to the trout farm and find a game pod left for them. She ports into the pod, but something goes wrong. Ted cuts her link to the pod, and she begins to bleed out. Yevgeny arrives and burns the pod, which releases deadly spores. Allegra stabs him, and the farm catches on fire. They awake back in the ski lodge. Allegra's pod has caught the disease from the game.
She injects the pod with a spore disinfectant, then sees Ted's bio-port is infected, too. She realizes Kiri installed an infected bio-port. She inserts a disinfectant pod his port, and says they cannot play for awhile. Suddenly the ski lodge is attacked, and the game cashier arrives, talking about freedom, and destroys the pod. Ted realizes they are still in the game.
Outside, a battle rages, and the cashier talks about the victory of reality (the death of eXistenZ). He points a gun a Allegra, but Kiri shoots him from behind. Kiri explains that he copied the game, and tries to recruit Allegra to Corticle Systematics. Allegra shoots Kiri. Ted points out that she's committed murder, then tries to kill her. Allegra triggers the bomb she inserted into Ted's bio-port and celebrates, thinking she's won the game.
Allegra and Ted awake back in the seminar, and the group de-briefs, applauding Ted and Allegra. The session proctor, Merla (Sarah Polley) tells everyone they will get a discount on the next game, transCendenZ. We realize Allegra was only playing a part of a game designer, and that Yevgeny is the real designer.
Yevgeny tells Merle he is nervous about the anti-designer theme. Ted and Allegra shoot Yevgeny and Merle, then shout "death to transCendeZ!". The Chinese waiter asks, "are we still in the game?"