Patrick comes to Clementine's house and finds her completely distraught. She keeps saying that "Nothing makes any sense," and he comforts her. Clementine decides, manically, that they have to go to Boston and see the frozen Charles. Meanwhile, back at Joel's apartment, Mary Svevo and Stan are having a drunken dance party on Joel's bed. The phone rings and Patrick's voice comes through the machine - he tells Stan that he's not coming back, and Stan is fine with it. Back at Clementine's apartment, Patrick pulls a sheet of paper out of his backpack - it's a love letter that Clementine wrote to Joel with an illustration of two potato dolls "Lying on the Charles River." He hides the letter before Clementine can see it, and pulls a gift out of his backpack - it's the red wrapped box that Joel had bought for Clementine before he knew she had erased him.
Clementine pulls a necklace out of the box and she genuinely loves it. She's impressed that Patrick knows her taste. Cut to Clementine and Joel snuggled under her quilt. She asks him if she is ugly and tells him a story from her childhood - when she was 8, her favorite doll was ugly and she named it Clementine. She would yell at the doll to be pretty. Joel tells her she's pretty and kisses her. Suddenly, blackness closes in on the frame and in his mind, Joel begs Dr. Mierzwiak to let him keep this memory, but it disappears along with the others.
Meanwhile, on the Charles River, Clementine and Joel hold hands. He tells her he has never felt this happy before. Suddenly, the memory is gone and they are lying on the concrete while commuters stream by them. Clementine disappears, and Joel is all alone. He looks up at the sky and begs to "call it off." Stan is now in his underwear, too, and he and Mary are still dancing. Joel's mind is screaming to stop the procedure but of course, they cannot hear him. Within his memory, Joel pulls Clementine to her feet and insists that they have to stop this. They race through his memories, desperate to find one that has not been mapped. Joel even goes to his memory of Dr. Mierzwiak, but he cannot do anything. Digging deeper, he remembers seeing Patrick at the Lacuna offices and makes the connection - Patrick has stolen Joel's things and is using them to seduce Clementine.
Patrick and Clementine are lying beside each other on the Charles River, just as she had done with Joel. Patrick recites Joel's words back to her, and Clementine sits up, urgently announcing that she wants to go home. She walks off the ice, leaving Patrick to chase after her in the darkness, calling after her. Cut to Joel, standing in the same place in daylight, crying out to Clementine, "They're erasing you!" She springs out of the leaves and scares him. He tells her that he made a mistake by hiring Lacuna, and that he's asleep so he cannot stop it. He lies on the ground and tries to wake himself up. Suddenly, he does wake up and hears Mary and Stan shrieking in his apartment. Mary and Stan don't notice that Joel is awake.
Now, Clementine and Joel are inside his memory. Clementine gives him the idea of taking her somewhere within his memories where she doesn't belong, where they can hide from the mapping until morning. Cut to Joel's childhood memory of splashing in the rain. The rain starts pouring on Joel and Clementine in the living room, meaning that they have successfully managed to find their way into Joel's childhood memory. Cut to a miniature adult Joel hiding under his childhood kitchen table. Clementine is dressed in a 1970s outfit, standing in the Barish's kitchen. She is now "Mrs. Hamlin," and is helping Joel's mother. Little Joel whines that his mother doesn't pay attention to him and he's afraid of being alone. Here, Joel and Clementine are successfully hidden from the memory erasure.
Meanwhile, Stan and Mary are huddled up, naked, under a blanket on Joel's easy chair when an alarm goes off on the system - it has stopped erasing Joel's memory. Stan anxiously realizes that Joel's "off the map." Mary starts panicking, and Stan tries to keep her quiet; she is clearly still stoned and suggests that they call Howard. Stan desperately agrees and makes the call. Dr. Mierzwiak answers the phone and realizes that he has to go over to Joel's apartment. Stan tries to get Mary to leave but she won't.
In Joel's mind, Little Joel is still under the table, crying that his mother won't pick him up. Clementine tells him to come see her in the morning and tell her about their relationship. Joel tells Clementine that Patrick is copying him, but since this version of Clementine is only in his memory, she has no idea what he's talking about. The real Clementine and Patrick are driving back from the Charles River, and Clementine appears to be completely manic. Patrick continues to compliment her, but she's upset and frantic. Mary Svevo and Stan prepare for Dr. Howard Mierzwiak's arrival, trying to pretend they are not stoned. Dr. Mierzwiak arrives, remaining calm while he examines the system. As Dr. Mierzwiak and Stan get to work, Mary teeters around, trying to be helpful.
Joel's mother sings "Oh My Darling, Clementine" while bathing a small adult Joel and small adult Clementine in the kitchen sink. Clementine says she's never seen him happier. Dr. Mierzwiak, however, cannot understand why Joel has wandered so far off the map. He zaps the memory, and Joel is sucked out of the sink. The real Joel, in his apartment, wakes up. His eyes are open but he can't move. Dr. Mierzwiak gives him an injection, and a single tear falls down Joel's face. He falls asleep again, and finds himself in a memory of going to a drive-in movie with Clementine. Joel is no longer hidden - he is back on the map. They are parked outside the theater without sound and make up their own lines for the movie, laughing. The memory starts to disappear, and they run as fast as they can, but Stan keeps finding the memories and eliminating them.
Clementine tells Joel to hide her somewhere really deep - under humiliation. In an effort to hide Clementine in his most humiliating memories, Joel lies in bed, masturbating, with Clementine beside him, and his mother walks in. Clementine laughs. It's not enough, though - Joel must find an even deeper place. He takes Clementine (who is now also a child) to another childhood memory - where Joel is holding a hammer over a wounded bird while the kids around him chant and jeer. Joel succumbs to their bullying and smashes the bird. Clementine rescues him from the young bullies and they go back to his childhood house, which also disappears. Dr. Mierzwiak says he's gotten the hang of finding Joel and eliminating the hidden memories. Joel and Clementine play-fight in bed, but she disappears. They run along the snowy beaches at Montauk and come upon a big green house, but keep playfully tackling each other to the ground - and then, Clementine is gone, once again.
Patrick violates the delicate trust that Joel places in Lacuna, Inc and uses Joel's most personal feelings to manipulate Clementine. The fact that she never really falls for Patrick shows that the love she and Joel shared was deeper than the things they gave each other or the physical embodiments of their relationship. In the same vein, both Joel and Clementine feel aimless and confused even after the procedure is complete, so even though their memories have been erased, the pain they have caused each other still lingers - but it's undefinable. Both feel something is missing (especially Joel), but neither can figure out what it is.
There are many different versions of both Joel and Clementine in the film (and Mary Svevo, too). There is pre- and post-erasure Joel, pre- and post-erasure Clementine, and then the versions of each of them that exist in Joel's mind while his memory is being erased. Clementine's ever-changing hair color helps the viewer keep track of which version we are watching. It is important to keep in mind that while inside Joel's memories, the versions of him and Clementine are subjective to Joel. As his bad memories disappear, his vision of Clementine also becomes much more sympathetic.
Joel leads (his version of) Clementine into the darkest recesses of his mind, hoping to hide her from Dr. Mierzwiak. In order to escape the memory-zapping machine, Joel is forced to show Clementine his most humiliating and vulnerable memories. This is ironic, because one of the reasons Joel and Clementine grew apart was his inability to communicate. However, in this moment of desperation, he has no choice - he either has to take Clementine into these dark places of his soul or let her go. It is a moment of growth for him - he is no longer the bitter, angry Joel who wanted to shut Clementine out of his heart and mind forever.
Meanwhile, as Dr. Mierzwiak finds Joel and Clementine hiding in memories unrelated to their relationship, Joel loses those memories as well. He no longer will have the memory of his mother singing "Oh My Darling, Clementine," or of his Huckleberry Hound doll, because those are inextricably linked to Clementine, even though she was not there. By losing his memories of Clementine, Joel loses major chunks of his own personal narrative - pieces of himself.
Michel Gondry's realistic visual style is part of what makes Eternal Sunshine so memorable. According to cinematographer Ellen Kuras, Gondry "felt that the more real the film looked, the more [the viewer] would believe it when the memories melted into reality" (Pavlus). Gondry creates these transitions through design, lighting, and his actors' performances. Kuras says that Gondry wanted to "[call] back to early cinema, where magicians were using live-action practical effects in order to change time and space. He didn't want them to look or feel completely seamless" (Pavlus).
For the scenes inside Joel's childhood memories, production designer Dan Leigh actually built oversized props and relied on forced perspective to make Jim Carrey look child-sized under the table. In the shot where Joel and Clementine are bathing in the sink, they actually built a huge kitchen sink. The real-life wackiness of these sets encouraged authentic responses from Jim Carrey and Kate Winslet, who sometimes had trouble keeping track of where their characters were and if what they were seeing was supposed to be real. This confusion worked in the film's favor, because Memory-Joel and Memory-Clementine are making up their plans on the fly - they are running away from an enemy they cannot even see.