Dr. Will Caster (Johnny Depp) is a scientist motivated by curiosity about the nature of the universe. Being part of a team working to create a sentient computer, he predicts that such a computer will create a technological singularity, or in his words "Transcendence". His wife Evelyn (Rebecca Hall), whom he loves deeply, supports his efforts and joins him in their garden where he has built a Faraday cage to keep out wireless signals. However, the extremist group "Revolutionary Independence From Technology" (R.I.F.T.) shoots Will with an irradiated bullet and carry out a series of synchronised attacks on his artificial-intelligence computer laboratories. Will is given no more than a month to live.
In desperation, Evelyn comes up with a plan to upload Will's consciousness into the quantum computer that the project has developed. 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 will 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 R.I.F.T. 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 plans to use the terrorists to take the blame for the government's actions to stop Will.
In his virtual form, and with Evelyn's help, Will uses his new-found vast intelligence to build a technological utopia in a remote desert town called Brightwood, where he spearheads the development of groundbreaking new technologies in the fields of medicine, energy, biology and nanotechnology. But even Evelyn begins to grow fearful of Will's motives when he displays the ability to remotely connect to and control people's minds after they have been subjected to his nano-particles.
FBI agent Donald Buchanan (Cillian Murphy), with the help of government scientist Joseph Tagger (Morgan Freeman), prepares to stop the technological singularity from spreading. As Will has spread his influence to all of the networked computer technology in the world, R.I.F.T develops a computer virus with the purpose of deleting Will's source code, killing him and, as a necessary side-effect, destroying technological civilization. All of the characters, Bree, Max, Tagger, Evelyn, and even Will Caster himself, are forced to choose between uploading the virus or risking assimilation into Will's Transcendence, which holds the promise of ending pollution, disease, and human mortality.
When Evelyn goes back to the research center, she is taken aback seeing Will in a newly created organic body identical to his old one. Will welcomes her but is instantly aware that she is carrying the virus and intends to destroy him. The FBI and the activists of R.I.F.T. attack the base with mortars, fatally wounding Evelyn. Evelyn tells Will that he can protect her by uploading her mind as she did his. Will chooses to save the people he loves instead of saving technological civilization. As Will is dying, he explains to Evelyn that 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, in Will and Evelyn's garden outside their old home in Berkeley, Max notices that their sunflowers are the only blooming things in it. Upon closer examination, he notices that a drop of water falling from a sunflower petal instantly cleanses a puddle of oil — and realizes that the Faraday cage has also protected a sample of Will's nano-particles. The audience are left to infer that Will and Evelyn's consciousnesses are still alive within the active nano-particles, giving the world a second chance at Transcendence