There's a theory on Rian Johnson's official forum that the The Brain only exists inside Brendan's mind. While Rian will neither confirm nor deny the theory, he has said it is "without a trace of irony, my favorite post on the forum."
The director was asked about his frequent shots of birds and feet in the movie. "'Birds and Feet' could be an alternate title for the movie," Rian Johnson joked. " The birds were definitely a little nod to The Maltese Falcon (1941), but it has more to do with shooting in San Clemente, a little beach-town in Orange County. It's my hometown actually, and we shot it at my high school. That town is full of birds, full of seagulls. I grew up surrounded by them and I knew that shooting there, we were going to be surrounded by them, so it kind of made sense to make that some sort of ongoing motif in the movie. The feet thing, I just personally really like shoes as a design element for a character. They can give you a very instant snapshot of the essence of that character. Brendan with his good solid, no-nonsense weathered shoes, or Emily, with shoes that were these beautiful delicate little things that now are all beat-up."
Writer/director Rian Johnson first wrote the story as a novella, in the style of Dashiell Hammett, before turning it into a screenplay. Both the novella and the original script are available for free on his official website.
In his meeting with Trueman, Brendan refers to a teacher "Kasprzyk" as being "tough but fair". Mrs. Kasprzyk was an actual teacher of English (including Advanced Placement English) who was largely known as being tough but fair at San Clemente High School, the school where the movie was shot.
The music score was composed by Rian Johnson's cousin, Nathan Johnson, with additional support and music from The Cinematic Underground. The score hearkens back to the style, feel and overall texture of noir films. It features traditional instruments such as the piano, trumpet and violin, and also contains unique and invented instruments such as the wine-o-phone, metallophone, tack pianos, filing cabinets, and kitchen utensils, all recorded with one microphone on a beat-up Apple PowerBook. Since Nathan Johnson was in England during most of the production process, the score was composed almost entirely over Apple iChat, with Rian Johnson playing clips of the movie to Nathan Johnson, who would then score them. The two later met in New York to mix the soundtrack.
The horn signal Brendan instructs Laura to give him (long, short, long, short) is the same as the doorbell signal Sam Spade tells Brigid O'Shaughnessy he'll use in The Maltese Falcon (1941). Brendan's earlier line to Laura, "Now you are dangerous," is taken from the film as well.
The opening scene, with Brendan looking at Emily's body, is very deceptively shot. What appear to be POV shots of Emily's body are in fact something else. Director Rian Johnson says, "Brendan's eye-line never changes. We see him ostensibly looking at different details each time, but that's never cued by eye movement. Those inserts aren't from the angle at which he's viewing them. From where he is, her feet should be at the top of the frame; instead, they're at the bottom, shot from her other side. The other two shots are likewise reversed. You could call that an error, I suppose, but coupled with the fixed eye-line, what it suggests is that Brendan can't process what he's seeing. It's so unthinkable to him that he can only take in tiny portions at a time. He's abstracted the sight of her into objects. The images are technically 'wrong,' but that contributes to the scene's overwhelming sense of wrongness.I know that when I see something traumatic, I don't really process it in the moment, but I store it with an intense amount of detail and then watch the memory of it very carefully. Those disconnected, weirdly beautiful pieces of Emily are not what Brendan would see from his vantage point, but they feel like what he'd remember from the scene."
Director Rian Johnson was asked by a critic, who first saw the film at Sundance, why he felt the need to go back and add the flashback title card (that reads "Two Days Previous") when the film premiered without one. "For years, I've told you you're crazy, and stuck by my guns with the flashback title," Johnson says. "But I've finally come around on this, and I think if I made the movie now, I'd drop that 'Two Days Previous' and let the filmmaking tell the story. But I do have one very strong case for it: There's an elegance and a cleverness to the flashback being told without the title, but just from a storytelling point of view, there's real value in knowing that when we hop back, it is only two days. Without that title, I agree that we'd all know we had flashed back, but it could have been six months previous. Two days gives it all an urgency and sense of immediate dread. When Brendan and Emily meet up, we know the next time he sees her will be in that tunnel." He was also asked why he changed the font of the title card, to which he replied, "The font of the main title, I have no excuse for. The cursive one was better, and I honestly can't remember why we changed it."
The filmmakers had filmed a version of the film scene with the playing field all muddy and damaged. When they came back to film more of the scene they discovered that the school had refurbished the field and it was now perfect and bright green. That's why most of the shots in the scene are angled upwards to hide the field from view.
The lack of classroom scenes in this high school film was much commented after the movie's release. While there originally was a scene set in Brendan's classroom, Rian Johnson had to re-write it to avoid a location change. This scene was the one where Brendan goes through the notebook he takes from Emily when they meet; in the original script, this happened while a teacher explains something in the background.
To cheaply create the effect of something coming out of the tunnel and jumping up in the observer's face, the dream sequence in which Brendan sees Emily coming out of the tunnel is shot in reverse. You can see this because the water appears to be flowing out of the tunnel, while in all the other shots, it's flowing in.
In the credits, a song is listed titled "Brain Hammer", credited as "Written and Performed by The Hospital Bombers Experience" and "Courtesy of Amalgamated Conglomerate Music Inc." It refers to the song that is playing in Tug's car when Brendan rides in the trunk, which is in actuality "me chugging some noise into Protools at 2 in the morning with my electric guitar," according to director Rian Johnson. (The band name is a reference to the song "The Best Ever Death Metal Band in Denton," by The Mountain Goats, a favorite of Johnson's. When bandleader John Darnielle saw this reference, he contacted Johnson, and Johnson has since directed two music videos and a concert DVD for The Mountain Goats.)
Barring the two establishing shots, the entirety of the scene at "Coffee and Pie, Oh My!" was actually shot somewhere behind the San Clemente High School, the same school that was used in much of the film. This is because the owners of "Coffee and Pie" initially didn't realize that the crew would take up parking spaces when shooting dolly shots for the scene.