Recursion and Destiny
The film demonstrates that the problem with Dr. Mierzwiak's procedure is that it only functions on a superficial level. It erases concrete memories, but it fails to address the basic tendencies of the characters and therefore, history seems destined to repeat itself. Howard and Mary's relationship repeats itself. Although the procedure has removed all of Mary's memories of being in love with Dr. Mierzwiak, she still admires him and is attracted to him. Joel and Clementine are also drawn to each other after they have undergone the treatment. They both emerge from the procedure feeling hollow and lonely, but not understanding why. The implication is, then, that by erasing these painful memories, Dr. Mierzwiak's procedure also removes the potential for these characters to learn from their mistakes, leaving them destined to repeat old patterns, for better or for worse.
Memories
Michel Gondry says that Eternal Sunshine of the Spotless Mind is about memories. The film demonstrates that a person's memories make up a significant part of who he or she is. Memories, even painful ones, are vital to these characters and the decisions they make. They are not easily extricated from one's life. Removing the characters' memories is not foolproof; the procedure ignites its own thread of drama and turmoil. In his most restrained and believable performance yet, Jim Carrey captures the entire gamut of Joel's emotions: his regret over choices made and careless things said, his growing desperation to save what little of Clementine remains in his mind, and his growing realization that even if he no longer loves her, or what their relationship had become, he could still love his memories of her. He also learns that some relationships cannot be erased, but must be resolved, and through his own mental conversations with his memory of Clementine, a wistful closure is attained, even as his memory of her fades.
The Nature of Attraction
Eternal Sunshine of the Spotless Mind demonstrates the rift between immediate attraction and a successful relationship. Without the memories of each other, the two main couples (Mary and Howard, Joel and Clementine) still feel the initial lightning bolt of attraction they felt when they first met (the first time). In this way, the procedure takes the characters backwards in their emotional growth, instead of the intended result of helping them move on. Mary, unaware that Dr. Mierzwiak has already broken her heart, reads quotes in an attempt to impress him. Joel is taken by Clementine's spontaneity (again) when he is feeling listless and lonely. At the end of the film, Joel tells Clementine, "I can't see anything I don't like about you," to which Clementine replies, "but you will." Is this knowledge enough to keep them apart? Even though they have heard these tapes detailing their bitter breakup, they are clearly attracted to one another - and it all depends whether Joel and Clementine decide to listen to their heads or their hearts.
Regret
Joel decides to have Clementine erased from his memory in a rare impulsive moment, driven by anger and hurt. However, he starts to regret his decision midway through, once he realizes how much he cherishes the memories of their relationship. In fact, by watching their relationship from a place of an observer, Joel realizes all the things he did wrong. He learns things about himself, and is able to repeat certain experiences in his mind, making different decisions or voicing his desire to have made opposite choices. Clementine is inherently impulsive, leading her to say and do things that she immediately regrets. Unfortunately, though, Dr. Mierzwiak's procedure proves too seductive, leaving Clementine unable to learn or grow from her rash decision to erase her two-year relationship with Joel. Mary's regret at having the procedure done is so immense that she immediately takes action to make sure that Lacuna's other patients do not suffer through the same fate as she has - experiencing the same heartbreak twice.
Conscious vs. Subconscious
The versions of Joel and Clementine that Joel sees in his memory are not real, but they are interpretations or projections of the real people. Therefore, the conciliatory conversations they have over the course of the film are essentially a figment of Joel's imagination. In an interview, Michel Gondry described having conversations with his dying father in his mind, and thought it tenuously possible to have subconscious interactions with someone you know really well. Joel's mental version of Clementine is not too far off from the real Clementine, a synthesis of her mannerisms, effects, and reactions over the two years they spent together. Nevertheless, Joel's subconscious self finds an element of closure in his relationship with Clementine; and his anger dissipates, leaving him with her final message: "Meet me in Montauk." His conscious self then takes the instruction, so Joel and Clementine are able find each other again.
Denial
Dr. Mierzwiak's procedure is a scientific experiment in denial. By removing all the physical memories of the person, the patient emerges believing that the pain never existed. However, just because Joel and Clementine don't remember their relationship, that does not mean that it did not happen. Lacuna Inc. has a rather weak system of dealing with the potential of their patients learning about memories they have had erased - they simply send form letters asking the patient's friends and family not to mention the relationship. Therefore, the burden of denial spirals outwards and has a ripple effect. In fact, Carrie and Rob's letter from Lacuna is the catalyst for Joel to approach Dr. Mierzwiak in the first place. Ultimately, as the film concludes, it becomes clear that even though Dr. Mierzwiak's procedure can eliminate the physical remnants of painful memories, it is little more than artificially enhanced denial. Erasing someone from one's brain does not remove the existence of that love from the heart, or from other's minds.
Communication
In many of Joel's memories, he regrets not being able to speak his feelings to Clementine. He can only write his frustrations down in his journal. Only in his most desperate moments can Joel share his deepest humiliations with Clementine. However, she (or at least the version of her in Joel's memory) is not fazed by Joel's darkest secrets. In fact, she supports him when he feels most alone. This indicates that if Joel had opened up to Clementine more, perhaps his anger and frustration would not have festered inside him until he reached a boiling point. Similarly, Dr. Mierzwiak cannot say anything to Mary when he feels her coming onto him again. He simply hopes that her crush will fade away - but he has information that she does not, and without that information, Mary is blinded by her admiration and love.
