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After a messy breakup Joel Barish opts to have his memory of the relationship erased using a state of the art medical treatment. However during the treatment he has second thoughts.
The title is a reference to the poem "Eloisa to Abelard" by Alexander Pope, which the character Mary quotes in the movie:
How happy is the blameless vestal's lot!
The world forgetting, by the world forgot.
Eternal sunshine of the spotless mind!
Each pray'r accepted, and each wish resign'd;
The movie opens with a shy Joel Barish, who decides on a whim to take a train to Montauk, New York. There he meets Clementine Kruczynski. Despite some initially awkward (yet familiar) conversation, the two hit it off in what seems to be an exciting, new relationship.
However, Joel and Clementine are ex-lovers who have had all memory of their relationship erased by Lacuna, Inc., a company that performs this procedure regularly, headed by Dr. Howard Mierzwiak. After the couple had a brutal fight regarding a car accident, Joel receives a letter from the company informing him that Clementine has had the procedure done, which prompts him to do the same.
He removes everything that reminds him of Clementine from his residence, Lacuna interviews him and maps his brain to all memories of Clementine. Then, two employees of Lacuna, Stan Fink and Patrick come to his apartment while he is asleep to perform the erasure.
The narrative then enters Joel's mind, as he re-experiences his memories of Clementine in a dream-like state (e.g.: the background loops as he is running past it, some images are distorted). The memories are triggered in reverse chronological order, starting from the fight, which started when Clementine wrecked his car after a night of drinking. At first, when the memories are being erased, Joel seems to be relieved that he is getting rid of them.
Confused by him
While Joel is going through this procedure, Mary (the Lacuna receptionist) comes to visit the two employees. Patrick takes this opportunity to reveal to Stan that he is now dating Clementine, and wants to leave to see her. He is using Joel's old things to impress her, and referencing lines and quotes from Joel's journal, which disturbs Clementine, although she isn't clear why.
Meanwhile, Joel begins to enter earlier, more pleasant memories of his relationship with Clementine. Even though he is aware what is happening, he tries to enjoy the time he is spending with his recalled version of his former lover. At one point during a very intimate memory where he is comforting Clementine when she is in emotional duress, he realizes that he does not want to forget.
Burried in some memory
The rest of Joel's time in his mind is spend trying to figure out how to stop the process and keep Clementine in his thoughts. He attempts (successfully) to open his eyes, and then tries to bury Clementine in his other memories, fighting against the brain scanner which is now erasing other memories from Joel's childhood as he recalls sad, shameful, and some extremely early memories as a toddler.
These abnormalities cause Stan to panic and call Howard in the middle of the night, who comes and tries to fix the problem. Although they are able to get Joel's mind back on track, Mary attempts to seduce Howard, who is then caught by his wife. It is revealed to Mary that she and Howard have a history, which has been erased from her memory. This prompts Mary to go back to the firm and send out all the Lacuna records of the erased memories to their clients.
Back in Joel's mind, the last memory of Clementine, the first day they met, has finally come. He is dreading losing the last remnant of her, and as the house they were in begins to fall apart, Clementine whispers to Joel: "Meet me in Montauk". He wakes up, and chronologically, this is point at which the movie started.
Clementine receives her Lacuna records shortly after the re-encounter, and Joel reacts as if it is some kind of prank. But he finds his own recorded Lacuna interview when he gets home, and Clementine is there to hear it. They listen awkwardly for a beat, as Joel apologizes for the harsh things he says about her, which neither of them can remember. The movie ends as they decide to stay together, despite knowing how it will inevitably come to pass.