Legendary Hong Kong stunt coordinator Woo-Ping Yuen initially refused to work on the film. Even after receiving the script, which he liked, he hoped that by asking for an exorbitant fee, it would turn off the Wachowskis. It didn't. He next formulated what he considered an impossible request. He said that he'd agree only if he had complete control of the fights, and that he trained the actors for four months before they shoot. The Wachowskis complied with his request.
After the lobby shoot-out, the camera pans back, showing the aftermath of the gunfight in the lobby. During this, a piece of one of the pillars falls off. This happened by coincidence during the filming, and was not planned, but was left, since it seemed appropriate.
All scenes that take place within the Matrix have a green tint, as if watching them through a computer monitor, while scenes in the real world have a blue tint, blue was also used at a minimum in the matrix scenes, since the directors thought blue was more of a real world color despite, ironically, blue being the least often occurring color in nature. The fight scene between Morpheus and Neo, which is neither in the real world, nor in the Matrix, is tinted yellow.
According to Costume Designer Kym Barrett, Trinity's costume was made with cheap PVC, because of the much tighter budget. Similarly, Neo's coat wasn't actually a very expensive fabric. It was a wool blend purchased for three dollars a yard.
Will Smith was approached to play Neo, but turned down the offer in order to star in Wild Wild West (1999). He later admitted that, at the time, he was "not mature enough as an actor" and that, if given the role, he "would have messed it up". He had no regrets, saying that "Keanu was brilliant as Neo."
For Keanu Reeves' scenes set in the real world at the start of the film, his costumes were deliberately shabby and ill-fitting, to suggest Thomas Anderson's feeling of not quite fitting into the world.
In the combat training program before Neo starts his furious attacks on Morpheus, he rubs his nose with his thumb and finger, similar to a mannerism of Bruce Lee before he attacks his opponents. The move was improvised by Reeves.
The filming of the helicopter scene nearly caused the film to be shut down, because they flew the helicopter through restricted Sydney airspace. Laws in New South Wales, Australia were changed to allow filming to proceed.
When Belinda McClory auditioned for the role of "Switch", she was only going for half the role. The character was originally planned to be played by androgynous actors. In the real world, it would be played by a male actor and in the Matrix be represented in a female form, hence the name "Switch". Warner Brothers refined the idea and McClory ended up getting a single female role in both environments.
The iconic sunglasses worn by the Matrix characters are from the cult-ish label Blinde, which prides itself on producing handmade glasses. The company's founder, Richard Walker, had to tender against large companies such as Ray-Ban and Arnette to win the film's sunglasses contract, and set himself apart by scratch-designing pairs of glasses based purely on the characters' unusual names. When his tender was successful, Walker was flown into Sydney where he spent the duration of the Matrix shoot custom-designing sunglasses for the cast in the back of an Oxford Street optometrist.
The Wachowskis harbored their vision for five and a half years, working through fourteen drafts of the screenplay. Although most studio executives who read the script loved their ideas, they had extreme difficulty imagining how this would translate onto the screen. The Wachowskis then hired leading illustrators Steve Skroce and Geofrey Darrow who created over six hundred storyboards. Executives were reportedly sold immediately after seeing the bold vision on display, and green-lit the film.
Shot almost entirely in Sydney, Australia, the location scouts found it very difficult to find burned-out, American-ghetto-looking locations. Many of the urban-decay locations had to be created from scratch.
Some personal information can be seen on Thomas Anderson's "criminal record" that Agent Smith glances at when he interrogates Neo: The last update to the file was July 22, 1998 Neo's date of birth is "March 11, 1962" Neo's place of birth is "Lower Downtown, Capital City" Neo's mother's maiden name is "Michelle McGahey" Neo's father's name is "John Anderson" Neo attended "Central West Junior High" and "Owen Paterson High" (named after the film's Production Designer). A few seconds later, a photocopy of his passport can be seen. There the place of his birth is CAPITAL CITY USA, his date of birth is the 13th of September 1971, the passport was issued on the 12th of September 1991 and will expire on the 11th of September 2001.
On the first day of shooting, Hugo Weaving suffered an injury to his leg. It was revealed to be a polyp that had to be surgically removed. For a while, there was a suggestion that the actor would have to be re-cast, but, by shifting the schedule around so that all of his stuntwork would take place at the end of shooting, Weaving was able to take the part.
The name of Morpheus' ship, the Nebuchadnezzar, is a Biblical reference to King Nebuchadnezzar II of Babylon, from the biblical Book of Daniel. King Nebuchadnezzar ("the Great") was famous for his conquests of Israel in Biblical times (specifically Judah and Jerusalem). He also built the Hanging Gardens of Babylon (one of the lost Seven Wonders of the Ancient World) for his wife. He has a dream he can't remember, but keeps searching for an answer, in Daniel 2:1-49.
Numerous sets of identical twins were cast as extras in the "Woman in Red" scene - in which Morpheus takes Neo through a computer simulation of The Matrix - to create the illusion of a repeating program. Example: the tall man with slicked-back hair and sunglasses in the opening shot is seen a few seconds later as a police officer writing a parking ticket.
The name of the company, for which Neo works, is Metacortex. The roots of this word are meta-, which according to Webster's means "going beyond or higher, transcending," and -cortex, which is "the outer layer (boundary) of gray matter surrounding the brain." Thus, Metacortex is "transcending the boundaries of the brain," which is precisely what Neo proceeds to do.
Before filming, the principal actors and actresses spent four months with martial arts experts learning the fight moves, from October 1997 to March 1998. The actors and actresses had originally thought that it would take just a few weeks.
When Tank is uploading the Martial Arts training to Neo, there is a shot of the computer screen as it scrolls through the various Martial Arts styles. The graphics have a computer image of a person and the title of the style below. The fifth one on the screen is entitled "Drunken Boxing". Woo-Ping Yuen, the fight choreographer for this movie, was director and fight choreographer for Jackie Chan's early hit, Drunken Master (1978) in which Jackie Chan's character masters the style of Zui Chuan, or Drunken Boxing. Some of the other Martial Arts fighting styles being downloaded are Jiu-jitsu, Savate, Kempo, Tae Kwon Do, and, of course, Kung Fu.
In the early stages of developing what was to become the famous Bullet Time sequence, Visual Effects Supervisor John Gaeta and Director of Photography Bill Pope constructed many gimbals and dollies in the hope of creating the effect the old-fashioned way. The original dolly they created for the camera, would be led around the action at a tremendous speed, but after many failed tests and broken dollies, they opted for computer graphics, which meant writing an entirely new program for the effect. However, the Bullet Time sequence does still use one very old-fashioned technique: still photography.
According to Don Davis, Johnny Depp was Lana and Lilly's first choice for Neo, but Warner Brothers wanted Brad Pitt or Val Kilmer. After Kilmer and Brad Pitt said no, Warner Brothers was willing to consider Johnny Depp, and then it came down to Johnny Depp and Keanu Reeves, whom Warner Brothers was pushing. Keanu was always really tuned in to the concept, and made a big difference in the casting.
The book Neo hides his computer discs in is called "Simulacra and Simulation" a treatise by Jean Baudrillard that explores the postmodern concept of simulation and hyperreality. The chapter where they're hidden is called "On Nihilism". Nihilism often involves a sense of despair coupled with the belief that life is devoid of meaning.
According to Weapon Provider John Bowring, guns for Keanu Reeves in the lobby sequence and the elevator sequence, were actually plastic lightweight weapons. They made a very faithful cast of the MP5K, which weighs about 150-200 grams, so that Keanu could carry them quite easily without worrying about the weight. Heavy versions of the same thing were also made, if they were to fall on the floor.
Sets from the film Dark City (1998), including rooftops, buildings, and other exterior sets, were used in this film. The rooftops that Trinity runs across at the beginning of the film are the same ones that John Murdoch runs across in Dark City. Both movies deal with humanity being kept in a carefully constructed illusion by outsiders, which prompted claims that The Matrix had effectively ripped off Dark City; in reality, the screenplay of The Matrix had been written long before Dark City was released.
Nicolas Cage turned down the part of Neo because of family commitments. Tom Cruise was also considered. Will Smith was approached for the role, but turned it down in favor of Wild Wild West (1999). He later said that turning down the role was the biggest mistakes he ever made.
The key of the beginning theme you hear at the beginning of every Matrix movie (rousing strings and horn blasts) ascends by one whole tone with each movie. The Matrix (1999) starts in the key of E, The Matrix Reloaded (2003) in F-sharp and The Matrix Revolutions (2003) in the key of G-sharp.
The actors and actresses of the film were required to be able to understand and explain The Matrix. Simulacra and Simulation was required reading for most of the principal cast and crew. Keanu Reeves stated that the Wachowskis had him read Simulacra and Simulation, Out of Control, and Evolutionary Psychology even before they opened up the script, and eventually he was able to explain all the philosophical nuances involved. Carrie-Anne Moss commented that she had difficulty with this process.
When Lana and Lilly Wachowski's screenplay for Assassins (1995) was being made for Producer Joel Silver, The Wachowskis brought Silver the script to this film. He was bowled over by their screenplay, but not by The Wachowskis' insistence that they direct the film themselves. He told them to cut their teeth by directing something else instead, which is why they made Bound (1996). The success of that lesbian crime thriller proved to be the calling card that The Wachowskis needed to earn the trust from Warner Brothers to direct this movie themselves.
The idea for the movie was created when The Wachowskis were thinking for some new story for a comic book series. They wrote the entire script before their first directorial venture Bound (1996), and worked on it up until the time of production.
Prior to the pre-production, Keanu Reeves suffered a two-level fusion of his cervical spine which had begun to cause paralysis in his legs, requiring him to undergo neck surgery. He was still recovering by the time of pre-production, but he insisted on training, so Woo-Ping Yuen let him practice punches and lighter moves. Reeves trained hard and even requested training on days off. However, the surgery still made him unable to kick for two out of four months of training. As a result, Reeves did not kick much in the film.
By filming in Australia, the film-makers kept the final budget at sixty million dollars. The movie would not have been green-lit by Warner Brothers otherwise, because it would have cost a record 180 million dollars for a U.S.-based production.
The film pays a huge homage to Lewis Carroll's "Alice's Adventures in Wonderland", although there are also references to Karl Marx, Franz Kafka, Zen, and Homer's Odyssey. One of the main featured works of literature is "Simulcra and Simulation" by the French philosopher Jean Baudrillaud. The book can be seen lying open in Neo's apartment, and was required reading for all the principal cast and crew.
Filming the scene when Neo slammed Smith into the ceiling, Chad Stahelski, Keanu Reeves' stunt double, sustained several injuries, including broken ribs, knees, and a dislocated shoulder. Another stuntman was injured by a hydraulic puller during a shot where Neo was slammed into a booth.
All of the references to street corners (for example, Wells and Lake) are real intersections in Chicago, Illinois, The Wachowskis' hometown. The subway train has signs for "Loop," another Chicago reference. The film however is quite obviously not set in Chicago or any other real city (though it was filmed in Sydney).
When Mouse is cornered by the S.W.A.T. team during the raid, the guns he pulls out are a pair of cam-operated, electrically-driven 12-gauge automatic shotguns with 25-round drum magazines, capable of firing at 900 RPM. They were built specially for the movie by John Bowring, the film's key armorer.
According to Costumer Gloria Bava, Neo's original coat was silver gray leather. It was changed because the directors wanted something that was able to billow and float. There is a reference in the script to "liquid sky"; a coat that would liquefy with the surroundings and billowy. Even putting a wind machine under the coat didn't move, because the leather was too heavy. Costumers finally changed the fabric.
To prepare for the wire fu, the actors had to train hard for several months. The Wachowskis first scheduled four months for training. Woo-Ping Yuen was optimistic, but then began to worry when he realized how unfit the actors and actresses were. Yuen let their body style develop, and then worked with each actor's or actress' strength. He built on Keanu Reeves' diligence, Laurence Fishburne's resilience, Hugo Weaving's precision, and Carrie-Anne Moss's feminine grace. Yuen designed Moss' moves to suit her deftness and lightness.
Due to Keanu Reeves' neck injury, some of the action scenes had to be re-scheduled to wait for his full recovery. As a result, the filming began with scenes that did not require much physical exertion, such as the scene in Thomas Anderson's office, the interrogation room, or the car ride, in which Neo is taken to see the Oracle.
According to Lana Wachowski, for the slow-mo bullet ripple effects, Sound Designer Dane A. Davis put bullets on strings and whirl them around his studio. Also he digitized raindrops against window panes to create the sound of the Matrix code.
When Morpheus is explaining "What the Matrix is" to Neo, he uses the phrase, "Welcome, to the desert of the real." This is a paraphrase from Jean Baudrillard's "Simulacra and Simulation", the hollowed-out book where Neo keeps his illegal software. The quote can be found in Chapter One - The Precession of Simulacra, Page one, Paragraph 2, "It is the real, and not the map, whose vestiges persist here and there in the deserts that are no longer those of the Empire, but ours. The desert of the real itself." NB: The American title of Baudrillard's book is Simulations. It was published by Semiotext(e) in 1983.
According to the inscription on the Nebuchadnezzar's core, the ship was "Made in the USA" in the year 2069. It also states that it is a "Mark III, No. 11" model, which is a possible reference to Mark 3:11, which reads "And whenever those possessed by evil spirits caught sight of him, they would fall down in front of him shrieking, 'You are the Son of God!'"
Hugo Weaving stated that the character of Agent Smith was enjoyable to play, because it amused him. He developed a neutral accent, but with more specific character for the role. He wanted Smith to sound neither robotic nor human, and also said that the Wachowski's deep voices had influenced his voice in the film. When filming began, Weaving mentioned that he was excited to be a part of something that would extend him.
Sandra Bullock turned down the role of Trinity, because she couldn't see herself acting alongside the actor the studio intended to play the role as Neo. This was before Keanu Reeves was cast, with whom she had worked on Speed (1994) and would work on The Lake House (2006). She later regretted this decision.
When Neo is meeting with the Oracle, the music playing in the background in her apartment is Django Reinhardt's "Nuages". Following this tune can be heard Duke Ellington's "I'm Beginning to See the Light".
For the "Ultimate Matrix Collection" DVD re-release, the film was given a totally new, clean DVD transfer to replace the grainy one that had been on DVD since 1999, and give it the clear, sleek look of the sequels, which had not been seen since the theatrical release.
During the Trinity rooftop chase at the film's beginning, two distinctive city skylines are noticeable. Nashville, Tennessee's BellSouth Building and L & C Tower are visible behind the Agents. San Francisco's TransAmerica and Coit Towers can be seen behind Trinity after she jumps past the Guns & Ammo billboard.
After Smith sends Neo flying backwards with a punch to the chest, Neo spews blood before getting back to his feet. Once he does, he taunts Smith in a fighting stance. The stance branches from the style Hapkido.
For the scene when Neo wakes up in the pod connected to the Matrix, the pod was constructed to look dirty, used, and sinister. During the testing of a breathing mechanism in the pod, the tester suffered hypothermia in under eight minutes, so the pod had to be heated.
The Wachowskis' approach to action scenes drew upon their admiration for Japanese animation such as Ninja Scroll (1993) and Akira (1988). Ghost in the Shell (1995) was a particularly strong influence. Joel Silver has stated that the Wachowskis first described their intentions for the film by showing him that animé and saying, "We wanna do that for real."
Hugo Weaving had to undergo hip surgery after being injured during fight training, which completely shifted the shooting schedule. Consequently, Weaving's fight scenes were completed at the end of the production, in order to allow time for him to heal.
Agent Smith refers to Cypher as Mr. Reagan during their meeting. This makes him the only character in the movie besides Neo to be identified by both their Matrix identity and their real world "handle" identity.
The Nebuchadnezzar was designed to have a patched-up look, instead of clean, cold and sterile space ship interior sets as used on films like Star Trek (2009). The wires were made visible to show the ship's working internals, and each composition was carefully designed to convey the ship as "a marriage between man and machine."
For the subway scene, the set was first planned to be shot in a real subway station, but due to the amount of the actions and the wire works, the decision was made to shoot on a set. The set was built around an existing train storage facility, which had real train tracks.
The dojo set was built well before the actual filming. During the filming of these action sequences, there was significant physical contact between the actors, earning them bruises. Because of Keanu Reeves's injury and his insufficient training with wires prior to the filming, he was unable to perform the triple kicks satisfactorily and became frustrated with himself, causing the scene to be postponed. The scene was shot successfully a few days later, with Reeves using only three takes. Woo-Ping Yuen altered the choreography, and made the actors pull their punches in the last sequence of the scene, creating a training feel.
Principal photography wrapped at 1:01 a.m., with the scene where the characters are inside the wall, climbing down. Principal photography took 25 weeks, or 118 days, which was almost a month over the 90 days that were initially allotted.
The Wachowskis had all the lead actors read "Simulacra and Simulation" by Jean Baudrillard, "Out of Control" by Kevin Kelly, and "Introducing Evolutionary Psychology" by Dylan Evans and Oscar Zarate in order to better understand the world of the movie. In the film, Neo actually hides his illegal computer files in a copy of Baudrillard's book.
There are many who might legitimately claim to have invented the time-freezing photographic technique used in the movie. It might have been Michel Gondry, who used it for the first time in a commercial (for an insurance company) and then in a video clip for Björk. It might have been architectural graphics artist Matthew Bannister, who, in his academic work, suggested that motion and time in video could be separated, and proposed an apparatus for doing it much like that used for the film (but who was unable to make it work with then-available technology), or even artist Tim MacMillan, who demonstrated the technique on British television in 1993. It may be that each of them, and others, invented it independently.
As of April, 2016 a research team at DARPA was working on a project which focuses on Targeted Neuroplasticity Training (abbreviated TNT) which involves the use of electrodes put at the base of the neck and the use of electrical impulses to influence a person's neurotransmitters. The purpose is to allow Agents to learn languages and other complex subjects in a fraction of the time. It is similar to Neo being plugged into the training program to learn complex skills faster, except not as medically invasive.
Sophia Stewart had a case pending against the directors, producers, and studios behind the Matrix and Terminator movie franchises, claiming that they were all based on a 35 page screenplay treatment she wrote in 1983 called "The Third Eye". Although the case was rejected because of the litigant's failure to present evidence in a timely fashion, Stewart continues to discuss her version of events online. For example, the "John Connor" and "Neo" characters are (she claims) the same individual in her treatment.
After reading the script, Carrie-Anne Moss stated that at first, she did not believe she had to do the extreme acrobatic actions as described in the script. She also doubted how the Wachowskis would get to direct a movie with a budget so large, but after spending an hour with them going through the storyboard, she understood why some people would trust them. She underwent a three-hour physical test during casting, so she knew what to expect subsequently.
Cypher, whose last name is Reagan, wants to be "important, like an actor," a wink to President Ronald Reagan. A reference to this is that in the same conversation, Cypher says that he doesn't want to "remember anything". President Reagan was diagnosed with Alzheimer's Disease.
William Gibson's novel Neuormancer was an influence on the film (in particular, use of the term "Matrix"). After watching the film, Gibson commented that the way that the film's creators had drawn from existing cyberpunk works was "exactly the kind of creative cultural osmosis" he had relied upon in his own writing. However, he noted that the film's Gnostic themes distinguished it from Neuromancer, and believed that it was thematically closer to the work of Philip K. Dick.
When Neo fights Morpheus in the construct, the three pieces of music that play on the score are termed the "Bow Whisk Orchestra" by Composer Don Davis. It consists of a semi-improvisational piece with Asian instruments by Davis, the song "Leave You Far Behind" by Lunatic Calm, and another piece by Davis called "Switch or Break Show". Both "Bow Whisk Orchestra" and "Switch Or Break Show" are anagrams of "Wachowski Brothers". Also, when Neo, Morpheus, and Trinity return to the building after visiting the Oracle, the piece of music that plays is called "Threat Mix". Later, when in the same building Morpheus fights Agent Smith, the musical piece is called "Exit Mr. Hat". Both "Threat Mix" and "Exit Mr. Hat" are anagrams of "The Matrix".
The antique television Morpheus shows to Neo in the construct is an AWA (Amalgamated Wireless - Australasia) Radiola "Deep Image" Model 209C or very similar model, circa 1958. Its bottom speaker section with fabric grille is missing, probably removed by set design to create a cleaner appearance.
The shot as Trinity tells Neo, "you know exactly where it ends", was filmed on Elizabeth Street (Sydney, New South Wales, Australia) looking north alongside CityRail's - Central to City Circle - train line from where Campbell Street also intersects with Wentworth Avenue. The white wooden scaffolding illuminated to the left was actually there before filming. Shot at night, the rain was added by a firetruck. Local street signs were pulled out and remained uprooted street-side for several days after location filming had moved on.
The song that Neo is listening to when Trinity contacts him is called "Dissolved Girl" by Massive Attack. Oddly enough, the song is not on the film's soundtrack, even though it was the first song ever played in the film and is part of a significant scene.
The first trace program gives a view of the City's area code, but the camera zooms in before it can be completely determined, leaving the phone number as (3?2) 555-0690. Three locations exist in the United States with similar codes: Chicago (312), Delaware (302), and the northwestern Florida peninsula (352). Since the original script indicates that the number is 312-555-0690, and there are numerous other references to Chicago in the film, we can assume that the area code is 312.
At the 72nd Academy Awards, Arnold Schwarzenegger presented the Visual Effects award segment which The Matrix (1999) won. A decade earlier Arnold Schwarzenegger starred in the science fiction film Total Recall (1990) which Schwarzenegger stars as a man who goes to the planet Mars to solve of the mystery of himself when a memory implant procedure of a holiday on Mars goes wrong. Like The Matrix, Total Recall is about the nature of reality and about a man whom gets caught up with rebels which he falls in love with a female rebel warrior. In both films, the film's protagonists at offered red pills which will return them to reality.
Janet Jackson was initially approached for the role of Trinity, but scheduling conflicts prevented her from accepting it. In an interview, she stated that turning down the role was difficult for her, so she later referenced the film in the "Intro" and "Outro" interludes on her tenth studio album "Discipline".
The film bears a couple of similarities to the "Terminator" films: The film takes place in a dark post-apocalyptic future, in which machines have taken over the world. Morpheus and a band of rebel warriors are fighting to free humanity from the machines and the Matrix computer program. Neo is believed to be the chosen one who will destroy The Matrix and end the war between man and machine. Neo, Morpheus, and Trinity wear sunglasses and leather outfits. Trinity rides a motorcycle in one scene. Neo works as an employee of a computer company and is also a computer hacker. Agent Smith, a law enforcement program, has the ability to change into the form of other individuals in The Matrix and one of the weapons Neo uses on the Agents is a Mini gun.
When we are introduced to Neo, he's asleep at his computer. Images are seen rapidly changing on the screen, one of which is the front page of an actual Arabic newspaper. Loosely translated, the title of the newspaper means "Midday". Additionally, the main body of the page is about the negotiations between Lebanese Christians and Syrian President Al Asaad in the late 1990s.
The bomb used in the elevator used a redundant pair of mercury switches. They are triggered by movement, which causes the mercury to touch a pair of contacts, completing an electrical circuit. These are also referred to in Lethal Weapon (1987).
In the last scene, in which Agent Smith's chasing Neo through a building, as Neo's looking for an exit, he runs through an apartment occupied by two old women (right after Tank said for Neo to go to his "other" left). On the television, is The Prisoner (1967), the iconic late 1960s television series, in which a secret agent (no name officially given) has been abducted, and awakens to find himself imprisoned in an unnamed village. The landmark series supposes how "we're all prisoners".
When Neo has a meeting with his boss at Metacortex near the start of the film, the boss talks about choices. The boss is called Rhineheart which may be a reference to Luke Rhinehart, author of "The Dice Man" - a book about choices.
There was a rumor that the studio had little fate in the project, and only gave the Wachowskis $10 million instead of the $60 million dollar budget that they had asked for. Allegedly, the directors spent that entire amount on the opening scene alone, which impressed the studio sufficiently for them to green-light the rest of the budget. This story was later discredited, although there was a hint of truth: when studio executives were unhappy with how the production moved along and threatened to intervene during filming, the directors and editor hastily compiled the opening scene and finished it with temporary sound and visual effects. The result was enough to keep the studio off their back for the rest of the shoot.
The trivia items below may give away important plot points.
The date stamp on the phone trace program in the opening sequence reads "2/19/98". The date stamp on the phone trace program in the closing sequence reads "9/18/99". This means that the events in the movie take place over exactly nineteen months.
When Neo gets in the car with Trinity for the first time, Switch refers to him as "coppertop". Coppertop is a slang for the Duracell Battery, which is the battery Morpheus shows to Neo as he explains how the human race became an energy source.
A deleted subplot reveals that Morpheus has previously believed five other people to be The One, all of whom died after attempting to fight the Agents. In The The Matrix Reloaded (2003), the Architect explains that there have been five previous versions of the Matrix before the current one, each with its own version of the One, meaning that Neo again has five predecessors.
A combination of practical and digital effects were used for the interrogation scene where Neo is implanted with the bug. A prosthetic stomach was used for the scene where the agents hold down Neo so that Agent Smith can activate the bug that digs into his belly button, notice the small indentation a few inches away from his navel where the plastic had slightly bent. A remote controlled device was also used to simulate the bug's tendrils that were squirming around once they were inside of his stomach. The bug itself was also a combination of CGI and an animatronic. The scene where it activates is CGI while the shot where it's squirming on his stomach is practical, when it's digging into his navel it's CGI.
In the interrogation scene, Neo's mouth is somehow melted shut before Agent Smith activates the bug that enters his body through his navel. Neo was still plugged to the system through the Machines ports so they control the ports I/O, his whole "body" at this point is just a computer avatar. It is created and maintained by the Machines behind the agents, and they can manipulate its form simply by altering the Matrix source code defining it, which is how they sealed his mouth shut.
Neo's mouth is melted shut during the interrogation scene, this motif is an intentional homage to the science fiction novel "I Have No Mouth, and I Must Scream" which served as one of the many influences for the film. The scene was accomplished with CGI and practical effects, his lips joining together and separating as gooey flesh before sealing shut is CGI while the rest of the shots were practical. Plaster and prosthetic makeup was used over Keanu Reeves' mouth to simulate the effect.