Dr. Will Caster (Johnny Depp) is a scientist motivated by curiosity about the nature of the universe, part of a team working to create a sentient computer. He predicts that such a computer will create a technological singularity, where everything will change, an event which Will calls "Transcendence". His wife Evelyn (Rebecca Hall), who he loves deeply, supports him in his efforts. However, a gang of luddite terrorists shoot Will with a bullet laced with radioactive materials which will quickly kill him.
In desperation, Evelyn comes up with a plan to upload Will's consciousness into the quantum computer that the project is working on. His best friend Max Waters (Paul Bettany), also a researcher, questions the wisdom of this choice.
Will's likeness survives his body's death and requests that he be connected to the Internet so as to grow in capability and knowledge. Max panics, insisting that the computer intelligence is not Will. Evelyn forcibly ejects Max from the building and connects the computer intelligence to the Internet.
Max is almost immediately confronted by Bree (Kate Mara), the leader of Revolutionary Independence From Technology (R.I.F.T.), the extremist group which carried out the terror attacks on the artificial-intelligence scientists and laboratories. Max is captured by the terrorists and eventually persuaded to join them. The government is also deeply suspicious of what Will's uploaded person will do, and plan to use the terrorists to take the blame for the government's actions to stop Will.
Will uses his new-found intelligence to build a technological utopia in a remote desert town called Brightwood, but even Evelyn, who joins him there, begins to suspect his motives.
FBI agent Donald Buchanan (Cillian Murphy), with the help of a government scientist Joseph Tagger (Morgan Freeman), prepare to stop the technological singularity from spreading. Eventually all of the characters, Bree, Max, Tagger, Evelyn, and even Will Caster himself, are forced to choose between the destruction of all advanced technology, and a return to a pre-technological world, and acceptance of transcendence, and with it an end to pollution, disease, and human mortality.
When Evelyn goes back to the research center, she is taken aback as Will - now in an organic body identical to his old one - is welcoming her; however, Will instantly realizes that she intends to destroy him, prompting the FBI and the activists of R.I.F.T. to start attacking the base with mortars. Evelyn tells Will that he could protect her by uploading her, but Will refuses at first. When a mortar fatally injures Evelyn, Will takes her inside while he commands the hybrids to defend them. Bree takes Max hostage, threatening to kill him if Will does not upload the virus and destroy himself - and Will accedes to her demands. Will, as he's dying, explains to Evelyn that he truly is Will, saying he did what he did for her; saving the planet was her wish, to learn the secrets of the universe was his. Then, the virus kills both Will and Evelyn, and a global technology collapse and blackout ensues.
Three years later, at Will and Evelyn's garden outside their old home in Berkeley, Max notices that their sunflowers are the only living thing in it. Upon closer examination, he notices that a drop of water falling from a sunflower petal into a puddle, which is polluted with oil, almost instantly cleanses it - and realizes that the copper Faraday cage Will installed to "protect" the garden from cell phone transmissions has also protected a sample of Will's nano-particles. Max infers that Will and Evelyn's consciousnesses are still alive within the active nano-particles, giving the world a second chance at Transcendence.