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Eternal Sunshine all goes down in a pretty crazy order: we start in the future, shift to a recent past, and then continue reverse-chronologically further back in time, only to end up in the present that continues to the future we already saw and beyond.
Because we're helpful, we're going to tackle everything as chronologically as possible.
It all starts when Joel goes to a beach party with his friends Rob and Carrie and meets this green-haired, orange-sweatshirted girl named Clementine (okay, maybe it really starts with Joel getting a bath in the sink when he's a baby, but we're skipping that part for now). Anyway, that night Clem breaks into a house with Joel, but Joel gets scared and leaves. Still, he's drawn back to Clem, and he goes to see her at Barnes & Noble, where she works and where they officially start a relationship.
We only know a little about the next two years, but they're mostly happy. There's a hike through the woods in the fall, a trip to a drive-in theater, a parade of elephants.
But eventually things stop working out so well. Joel and Clem lie in bed arguing about communication, and when the two eat out, Joel thinks they are the "dining dead." They argue about having a child, and they argue even more when Clem comes home late, having dented Joel's car. Clem leaves and shortly thereafter goes to Lacuna, a medical business specializing in erasing memories—and, well, she has Joel erased from her memory.
Joel buys her an early Valentine's Day present to make up for what he said to Clem, but when he goes to her work, he sees her kissing some random guy and acting like she doesn't know him. Confused, Joel goes to Rob and Carrie, who tell him about Lacuna.
Joel goes to Lacuna himself, finds out the truth, and returns determined to do to Clem what she did to him. He collects (almost) everything that he has associated with Clem, and the Lacuna professionals, Dr. Mierzwiak and Stan, map his Clem memories using these objects. That night, he takes a pill and crashes on his floor. Patrick (another Lacuna technician) and Stan come in and get to work erasing Joel's memories.
At this point, Mary, the Lacuna receptionist, comes over, and they all drink alcohol and get high. Patrick goes to see Clem—he's totally seducing her using Joel's mementos, which he stole from Lacuna—and she takes him out on a frozen lake. Patrick quotes Joel's lines, and Clem freaks out and goes home.
Meanwhile, Stan passes out and loses Joel, who is purposely hiding in an old unrelated memory being under a table and getting a sink bath (oh, the good ol' days). Stan calls Dr. Mierzwiak over, and he is able to work his magic to find Joel, who is now running around like a chicken with its head cut off trying to preserve his memories.
Mary seems to really like Mierzwiak, and when Stan steps out, she kisses him and starts crying. Just as Mierzwiak is doing a mixture of kissing and comforting her, his wife, Hollis, pulls up and shares the news that Mary and Mierzwiak already had a thing, but Mary has had her memory erased. Disturbed by the experience, Mary decides to send all of the previous Lacuna patients' records back to them, essentially giving them a part of their lives back.
After having the procedure, Joel wakes up and takes a trip to Montauk. He meets Clem, and they bond as if it were their first encounter. They end up at her house for drinks and go and lie on the ice together again the following night.
On the way back to Joel's place, Clem plays the tape of herself erasing Joel that Mary sent her. Joel thinks this is a sick joke and kicks her out of his car. Of course, Joel finds his own tape when he gets home, and when Clem comes over, she is equally upset by the mean things he says about her on his tape.
But as Clem leaves, Joel catches up to her and asks her to wait. They know that if they try a second time at a relationship, it might end up the same way, but they decide they don't care.
They'll go for it, anyway.