The Patriots

The Patriots, also known as the La-li-lu-le-lo and Cipher, were a secret organization that controlled the United States of America by the early 1990s. The group was formed to fulfill the ideal of a unified world that was envisioned by the legendary soldier The Boss and later sought to control the entire world to ensure this.

The beginning of the Patriots
The Patriots were originally formed in 1970 as the reorganized version of the American Philosophers, using funds contained within the Philosophers' Legacy. The Legacy was stolen from the DCI at the climax of Gene's rebellion by former triple Philosophers' agent Ocelot (under Zero's orders). Before killing the DCI, Ocelot proclaimed that [he and Zero] were going to "end [the Philosophers], take back what [the DCI] stole from [he and Zero], and carry on the spirit of the true patriot", explaining that it was, "all part of our plan to make the world [The Boss] envisioned a reality." After Ocelot's intense speech, he executed the DCI in a way that looked like a suicide. Zero later contacted Ocelot and invited him to form part of his new organization, the Patriots. Ocelot agreed under the condition that Big Boss (Naked Snake) joined the organization as well.

Afterwards, Zero recruited Big Boss and Ocelot, along with two FOX comrades (Sigint and Para-Medic) and former Chinese Philosophers' agent EVA. In essence, the six founding members were all directly influenced by The Boss, and all were directy involved in Operation Snake Eater either as field operatives or mission support. The group then began plans to reunite the world by governing it from behind the scenes. Zero used his influence to turn Big Boss into a messiah-like figure for the world to follow, though Big Boss grew to resent this puppet-like role. The views of the two men also began to differ, in regards to the interpretation of The Boss's will: Zero took the concept to mean control of the entire world by a group under a single will to ensure unification; Big Boss believed that The Boss wanted a world where soldiers were not used as tools by the government.

Les Enfants Terribles
In 1972, Big Boss was gravely wounded from a battle and fell into a coma. Afraid of losing the Patriots' idol, Zero carried out a secret project known as "Les Enfants Terribles", in which Para-Medic would use Big Boss's DNA to create a number of clones. With EVA serving as the surrogate mother, Solid Snake and Liquid Snake were born (a third son would be born at a later date). However, this proved to be the final straw between Big Boss and Zero, and the former left the organization with a determination to oppose them and later formed his own mercenary group in an attempt to carry out his vision of The Boss's dying wish.

After Big Boss left, EVA and Ocelot chose to remain with the group but began to drift away (although the latter remained a spy for them to keep an eye on the organization for EVA). Zero, Para-Medic, and Sigint stayed with the organization and became increasingly power-hungry. Para-Medic became a morally corrupt doctor as the head of FOXHOUND's medical staff and chief geneticist, organizing and developing the Patriots' genetic research programs. Even though military-based genetic therapy was banned under international law, the Patriots were able to get away with it secretly because the laws in question were simply declarations and not actual treaties. Sigint would abuse his position in DARPA by accepting bribes and would participate in the development of AIs. Zero would start to accumulate more wealth and information as his words would start to influence decision-making all the way up to the Oval Office. But he was also hopeful (at the time) that his former friend would rejoin the group in time.

In 1974, the Patriots (using the name "Cipher") recruited Pacifica Ocean to act as a triple agent within the CIA and KGB. Through Pacifica, they had KGB operative Vladimir Zadornov provide money and technology for Hot Coldman's Peace Walker Project, and the training for his rogue CIA unit, the Peace Sentinels. Pacifica also implies that the Patriots by that point had also garnered control of the NSA, CSS, NRO, and DIA. Cipher also contacted Kazuhira Miller with a business proposal to help expand Big Boss's Militaires Sans Frontières, and to have them unknowingly participate in the project. In addition, they also inherited Coldman's beliefs on machines ruling over humanity and would use the data from the Peace Walker project to develop AIs that would subtly control humanity at a later date.

Following the large military expansion of MSF and its defeat of Coldman, Cipher ordered Pacifica to hijack the newly constructed Metal Gear ZEKE and offer Big Boss the chance to rejoin the organization. Cipher intended that the MSF act as a deterrent against enemy forces while it steadily increased its own power, which had been the true purpose of the Peace Walker project. After Big Boss's refusal, Pacifica, under Cipher's orders, intended to frame the MSF as an extremist cult by using ZEKE to launch a nuclear warhead at the United States, which Miller had been unaware of. Ultimately, this plot failed when the MSF damaged ZEKE and prevented the nuclear strike, though Cipher intended to use Les Enfants Terribles as a future insurance policy.

Ground Zeroes
Afterwards, Cipher discovered Paz's survival, and, suspecting that her integrity as an agent had been compromised, had her detained at Camp Omega. MSF also discovered her survival, and likewise they later planned a mission to retrieve her so they could find out more about the group, as she was the only viable link to the group. Around the same time, Cipher also arranged for UN Nuclear Inspectors to do an inspection of Mother Base, which placed MSF at jeopardy of having their nuclear development program being discovered.

Post-Peace Walker
As time passed, the Patriots gained more and more control over the American government. During the 1990s, the Patriots, through the Pentagon, orchestrated genetic engineering tests on various United States soldiers during the Gulf War using Big Boss's genes. These experiments resulted in the Gulf War Syndrome as well as various Gulf War babies with various deformities. They covered up the activites by claiming that they were caused by exposure to depleted uranium rounds from various tanks.

During the Liberian Civil War, the Patriots retrieved a child soldier from a relief shelter, through a non-governmental organization. Having been left at the shelter temporarily by his commander, Solidus Snake of Les Enfants Terribles, the child was selected due to the hatred he had for himself, and his denial of what he was. The Patriots later subjected him to experiments relating to mind-control and memory manipulation, and would use him to further their goals in the future.

In May 1996, the Chief of Naval Operations died, resulting in the cancellation of a classified project concerning a new type of battle ship. As a result, the funds freed up within the Pentagon's Black Budget would later be used for ArmTech's development of a new Metal Gear.

Big Boss's coups d'etat
In the 1990s, Big Boss attempted coups d'etat against Zero, first in Outer Heaven, and then in Zanzibar Land. However, he was defeated both times by Solid Snake (his own son); Zero's insurance policy having paid off. Zero then had Big Boss placed into a nanomachine-induced coma, to imprison both his physical body and consciousness, and preserve him as the Patriots' icon. Infuriated by this, EVA and Ocelot secretly defected from the organization and schemed on how to destroy Zero and the other members who remained loyal to him. Meanwhile, Dr. Clark (Para-Medic) oversaw the gene research program which would eventually bear the Next-Generation Special Forces: genetically-enhanced soldiers, implanted with Big Boss' "soldier genes."

Entering the 21st century
Due to his increasing age and bitterness over Big Boss's betrayal, Zero became skeptical that his human subordinates would be able to successfully carry out his will. With his immense amount of money (and Sigint's assistance), he commissioned the creation of computer AIs (TJ, TR, AL, and GW) with a fifth head AI that would control the world, even after his eventual death. These AIs became Zero's successors of the Patriots. The AIs were formless, and alloted funds to specific R&D centers and other such companies under the Patriots control. The AIs were "a set of norms", a neural network in its simplest form, designed to decide and eventually manipulate the fate of the world. After the AIs were created, Zero went into hiding.

The Patriots, laying the groundwork for the eventual activation of these AIs, particularly GW's information control capabilities, also gave the populace and government organizations a program that was allegedly supposed to counteract the Y2K bug, that was distributed to all key governmental and military computer systems using full access to the internet, and then given to the civilian population in an OS. This program also contained a sub-program that would be activated once GW's information manipulation and control capabilities were completely installed at a later time. At some point later, JD was launched into outer space as a satellite and placed around space debris in orbit around Earth to make tracking it more difficult.

By the 21st century, the Patriots had achieved immense political power, effectively controlling America as a totalitarian regime. The organization would select who would serve as the President of the United States and would stage Presidential elections in order to please the American public, as well as tricking them into believing that as voters they had control over the government, that the nation was still being led according to the Constitution, and also utilized cut-outs when contacting the President with instructions. Presumably, they were also involved in regards to the NMD Program being a success in 2000 under Solidus's command.

In 2002, DARPA Chief Donald Anderson (Sigint) was heavily bribed by ArmsTech President Kenneth Baker to back the Metal Gear REX program and fund its development covertly, in order to overcome a global trend of military downsizing. A weapon such as REX would cause an immediate rift in the global power structure. REX was capable of launching a nuclear warhead without the need for a rocket propulsion system, making it undetectable by radar, and exploiting a loophole in anti-ballistic missile treaties. It could give any country in the world a first-strike capability that other nations would find hard to counter.

In 2003, EVA and Ocelot enlisted the assistance of Naomi Hunter and Gray Fox in order to have Dr. Clark killed. Gray Fox was able to exact revenge on Clark for all the years of torment he had suffered during her gene therapy experiments. Naomi later helped to cover up the incident by claiming that she had died in a lab explosion.

In 2005, DARPA Chief Donald Anderson and ArmsTech President Kenneth Baker were both present at the nuclear disposal facility on Shadow Moses Island, which had been used to construct Metal Gear REX in secret. The aim was to conduct test experiments of Metal Gear REX's nuclear launch capabilities (firing its rail gun) in a VR environment and retrieve the test data for the Pentagon.

Acting against the Patriots, U.S. President George Sears directly instigated the Shadow Moses Incident, by having his agent Revolver Ocelot incite Liquid Snake into revolting against the U.S. government. FOXHOUND, which had been overseeing the tests, took over the island facility with the Genome Army and hijacked REX. During a torture session, Ocelot killed Donald Anderson (who was aware of Ocelot's identity) and covered it up as an accident, succesfully eliminating another founding Patriot member.

The Patriots became involved in the incident through the Pentagon, with the use of the DIA's FOXDIE virus. They countered Sears's plan by using Solid Snake in an attempt to rescue Donald Anderson, also using him as a vector for FOXDIE in order to leave REX (along with the bodies of the Genome Soldiers) undamaged for retrieval. The DOD had also sent in Meryl Silverburgh to Shadow Moses prior to the incident, having anticipated its occurence, and used her to force Roy Campbell into cooperating in the mission. To exert their control over the operation, the Patriots utilized Secretary of Defense Jim Houseman, who took charge of the entire operation and who gave the order for Naomi Hunter to inject FOXDIE into Solid Snake. Additionally, DIA operative Richard Ames, who had oveseen the FOXDIE program, forced his ex-spouse Nastasha Romanenko into providing mission support for Snake, thus acting as the eyes and ears of the Patriots. Liquid, however, was aware of their involvement, and shortly after REX's destruction, Liquid threatened to kill them in a manner that will "make even the reaper's stomach turn" after revealing that he knew that they were listening in via Snake's Codec.

The Patriots eventually placed Jim Houseman under arrest, after he directly interfered with the operation by ordering a bombing raid on Shadow Moses, ruining the chances for a complete cover up of the incident. The Patriots also intended for Nastasha to die at the end of the incident, but Ames relented and gave her the FOXDIE data as well as the Shadow Moses Incident data to keep the Patriots from harming her, lest she leak all the data onto the web.

While Solid Snake defeated REX and Liquid, Ocelot retrieved REX's battle data for President Sears and later leaked the data via the black market. When details of the event became public, the Patriots removed Sears from office and planned to have him killed, though he escaped by going undeground with the help of Ocelot. In addition, they also fed the President succeeding him, James Johnson, a cover story that claimed that the development of REX was unsanctioned by them, and placed the blame squarely on Anderson's shoulders. The Patriots also secretly continued the experimentation on the Genome Soldiers after publishing a cover story that stated that they were reassigned to Pease AFB for "training" as well as being imprisoned, although rumors managed to circulate about the true reason for their imprisonment. In addition, the Patriots also arranged for Ocelot to sell the Metal Gear REX data onto the black market so the earnings (enough money to buy a decent-sized country) could be used for them to develop a new project.

Post-Shadow Moses
In June 2007, journalist Gary McGolden was supposedly captured by agents of the Patriots, after travelling to Shadow Moses while investigating the truth behind the 2005 incident, because of his having the disc containing sensitive information on the 2005 incident. According to his article, he was interrogated within a weather station, but was subsequently rescued by an "invisible savior."

By 2007, the U.S. Marines had initiated a project to build a new type of Metal Gear, in order to counteract the increasing number of Metal Gear derivatives being built after its specifications were leaked onto the black market. This new Metal Gear was Metal Gear RAY, though its development did not fall in line with the Patriots' plans, and the organization decided to reclaim RAY for their own. In addition, Philanthropy not only uncovered further evidence of their existence, but also evidence that they were involved in the creation of the United States Navy's version of Metal Gear.

In August 2007, the Patriots decided to eliminate the threats posed by both RAY's development and the anti-Metal Gear activities of the NGO Philanthropy. They leaked information on RAY's development to Philanthropy in order to lure out Hal Emmerich and Solid Snake, the latter of whom had become a hero in the wake of Shadow Moses. While Snake infiltrated the dummy oil tanker on which RAY was being transported, the Patriots monitored their Codec communication channels, though this was later discovered by Otacon. Patriot agent Revolver Ocelot took over the tanker with the help of Sergei Gurlukovich and his mercenary army, but he later betrayed them, sank the ship, and stole the RAY prototype (though he claimed to be "taking it back" ), framing Snake and Otacon in the process. For the Patriots, the incident was a success. The Patriots immediately sent a loaded oil tanker to the same location and sank it. This necessitated the construction of the offshore cleanup facility, the Big Shell, which was used to disguise the development of Arsenal Gear.

Arsenal Gear was the Patriots' tool for securing power over the United States and in the world. The Patriots hoped to use Arsenal as a way of shaping the "truth" to fit their agenda. Arsenal Gear served the sole purpose of housing GW, one of their proxy-AIs designed to censor and delete unwanted information that could loosen their grip on the United States. For instance, GW controlled information through the media, television and mainly the free flow of data from the Internet. This was a means to completely censor any data detrimental to the Patriots' rule. This is a method of memetic eugenics, in which memes were artificially selected for or against by GW. Emma Emmerich was the main engineer to the programming for GW.

After the Tanker Incident, the Patriots had also staged terrorist attacks, that would later be attributed to SEALs anti-terrorist squad Dead Cell, killing many of their own allies and civilians alike. This was namely done to have Dead Cell go renegade. In late 2008, the Patriots led an extermination campaign against Dead Cell that eliminated two members (Chinaman and Old Boy) while three members (Fortune, Fatman, and Vamp) survived, as part of the Patriot's master plan. They also manipulated the U.S. President, James Johnson, into defecting to Solidus Snake's Sons of Liberty terrorist group by feeding and denying his ambitions to become a full member of the Patriots, instead of a mere pawn for him to fill in the role of President Baker during the Shadow Moses Incident. At some point during this time, they also injected one of their agents with life-monitoring nanomachines that would take away the injected person's life if one of their pawns failed in a mission, to give Raiden additional leverage later on. They also recruited Fatman to become a plant to test Raiden's progress, although they weren't able to convince him easily, eventually necessitating the arrangement for Peter Stillman to be coaxed out of retirement as a way of getting Fatman to agree to their demands, as he wanted to murder his former mentor.

In April 2009, the Patriots staged their plan by manipulating the information that surrounded the Big Shell Incident, the Patriots had proved that they could manipulate world events. Their agent Raiden was sent in to test the exercise and forced Olga Gurlukovich (by holding her child hostage) to assist Raiden. Eventually, Rosemary, Raiden's girlfriend, admitted to her stance as a Patriot agent for the Patriots to keep tabs on Raiden, although she did legitimately fall in love with Raiden. She was eventually removed from the mission and used as leverage for Raiden later on after she admitted this.

After GW was infected with Emma's worm cluster, Liquid Snake (via a second personality in Ocelot's body) had Arsenal Gear crash into Manhattan in order to recover GW, killing many civilians and destroying national landmarks in the process. The master AI, while using The AI posing as Colonel Campbell as well as an AI posing as Rosemary, then contacted Raiden and, after hinting that there were more AIs than just GW, revealed to Raiden that the Patriots were formed as a sort of "non-corporeal consciousness" over the course of many years in the White House, comparing it to the formation and evolution of humanity itself. Using the data they collected from this exercise their AIs (such as GW) would be improved even more. They also explained that they intended to control humanity via the manipulation of information (or in its words, giving it context), as well as revealing that they actually lied to Ocelot in regards to the actual details of their plan, codenamed the S3 Plan, or at the very least telling him a half truth. The S3 Plan did not stand for "Solid Snake Simulation" but "Selection for Societal Sanity", which acted as an experiment for them to see if they could indeed manipulate humanity's personalities and memories. After explaining their plans as well as the reason why they chose Raiden, the master AI then told Raiden to kill the Patriot defecter Solidus Snake. Raiden refused, deciding that he has had enough being told what to do by the Patriots. Unfortunately, the master AI had already anticipated this action, and reminded him that Olga's child was linked up as well as revealing that Rosemary is linked the same way, threatening to kill Olga's child and Rosemary and their unborn child if he either failed or outright refused to participate. While goading Raiden to deliver the finishing blow, the master AI also hinted that the Patriots only viewed soldiers and humanity as tools and machines to be discarded after their usefulness had been expended. After Solidus was defeated, Snake told Raiden to find himself before joining Philanthropy, suspecting that the Patriots were most likely going to continue using Olga's child and presumably Rosemary as leverage against him.

After the Big Shell Incident, Philanthropy "traced" the Patriots using information retrieved from Arsenal Gear, but discovered that all twelve members of the Patriots had been dead for at least a hundred years (as early as the 1900s), and that "one of them was [Philanthropy's] biggest contributor." Snake deduced that the information retrieved from the Arsenal Gear was false; it was only a fake lead orchestrated by the Patriots. The names they discovered was most likely the names of the original Wisemen's Committee that founded the Philosophers.

The war economy
Originally, Zero intended for the AIs to create a unified state by using the military-industrial complex to make economics and politics uniform and devoid of free will, all in the name of Zero's megalomaniacal attempt to erase individuality. However, at an unknown point in their creation, the proxy-AIs began to deviate from that plan by undergoing a mutation that gave them a will of their own and enabled them to decide on a better way to accomplish their goals: war. They created the war economy and started a battlefield revolution similar to the industrial and digital revolutions that was described as "a new world without ideology, principles, or ideals, not even the thing [The Boss] treasured the most: loyalty. It was a colossal error in judgment – one Zero couldn't possibly have foreseen." To control the flow of information, they would control the economy, by influencing the outcome of these wars through the Sons of the Patriots system which would also allow them to control individual people. The Patriots planned to extend their control down to the civilian level, actively controlling and censoring people through nanomachines, such as the nickname "La-li-lu-le-lo." In this case, members of "the system" were under the Patriots's direct influence could not even mention the name "the Patriots" and were forced by their nanomachines to say the codename.

In 2014, Liquid Ocelot brought the five biggest private military companies to his control under a single mother company called Outer Heaven. The five companies together rivalled that of the U.S. military in firepower, and Liquid was preparing to unleash his insurrection and hijack the SOP system from the Patriots (now fully controlled by JD). To counter Liquid's plans, the Patriots managed to trick and manipulate Meryl Silverburgh and her group (similar to how they tricked Raiden in 2009) and enlisted Drebin 893 (who, unlike the others, knew of his stance as a Patriot agent) to assist Old Snake and Otacon in their mission to terminate Liquid Ocelot. However, the Patriots did not foresee that Snake and Otacon would destroy the Patriots themselves in the process thanks to the true nature of Liquid Ocelot's plan. The Patriots had Drebin inject an unassuming Snake with a new FOXDIE virus to kill the rival Patriot faction: Liquid Ocelot, should Snake fail to kill Liquid himself, Big Mama (a.k.a. EVA) if Snake crossed paths with her, and Big Boss, should he ever awake from his coma and meet up with Snake.

The Patriots were ultimately destroyed by the FOXALIVE virus (an opposite to the FOXDIE virus) created by Naomi Hunter and Sunny, who borrowed some code from the original virus created by Emma Emmerich to destroy GW, which would infect and terminate JD and the other AIs (TJ, TR, and AL) which ran the Patriots, ending them forever. However, Sunny managed to pick and choose parts of society vital to the survival of modern civilization, preventing the "world chaos" Liquid Ocelot predicted in his victory speech.

With the Patriots' AIs destroyed and Liquid Ocelot defeated by Snake, there was one more threat that needed to be eliminated: Zero, the man who started the entire fiasco and the main founder of the Patriots. Shortly after JD had been effectively destroyed, Big Boss awoke from his coma and found the location of Zero's stronghold. After arriving there, he discovered Zero was a mere shadow of his former self: a man, whose advanced years had put him in a vegetative-like state and who was kept alive solely by machines. Big Boss then wheeled him over to Arlington Cemetery, and after explaining to Snake (his eldest son) about the full story of what happened in regards to the Patriots, Big Boss euthanized Zero by cutting off his oxygen supply. Shortly thereafter, Big Boss died from the effects of the new FOXDIE virus within Snake, thus ending the Patriots for good.

Post-insurrection
After the fall of the Patriots, more people, including Courtney Collins and Kevin Washington, managed to find out about the Patriots' existence, as well as their ties in SOP being removed, although it was still in the minority. Even those who did know about the Patriots did not often state their existence publicly, largely because it would either result in them being seen by the public as crackpots, or in the offchance that they did believe them, it would have resulted in there being a massive global panic. Speculation on the Patriots did persist to some extent on the Internet, with some being very close to the truth, although they were dismissed by the mainstream as being "just another conspiracy theory." In addition, thanks in part to FOXALIVE, all the information the Patriots had covered up became exposed, including cyborg development techniques, which resulted in a surplus of cyborg development. When Courtney was briefed on the Patriots existence by Kevin during the former's orientation into Maverick, she initially thought he was trying to pull a "BS-detecting test" on her, although she quickly figured out otherwise.

Names
The Patriots were named after the colonial American Patriots, a group of colonists of the British Thirteen United Colonies, who rebelled against British Empire's control during the American Revolution. It was their leading figures who, in July 1776, declared the United States of America an independent nation.

"Cipher" was the name the Patriots had assumed in its early years during the Peace Walker Incident. The word Cipher in medieval times meant "zero", derived from the Arabic word ṣifr; also means "empty." In cryptography, a cipher is an algorithm for performing encryption or decryption — a series of well-defined steps that can be followed as a procedure; mirror the nature of the Patriots (an encrypted and hidden organization) and, later, of the proxy-AI (a series of norms and procedures).

The names of the AIs (aside from JD --the core AI--) were the initials of the four American Presidents whose likenesses appear on Mt. Rushmore. They shared these names with the AI pods of the 1970s Peace Walker project, which were the idea of CIA Station Chief Hot Coldman.

"La Li Lu Le Lo" was a term automatically substituted for "Patriots." Government and military officials and others under the Patriots' direct control were manipulated by nanomachines inside their bodies so that whenever they tried to say the word "Patriots," their mouths would actually form the words "La Li Lu Le Lo" to keep the information secret. The phrase was previously used as a password answer during Operation Snake Eater, when Major Zero directed Naked Snake to ask "Who are the Patriots?", in order to identify their KGB contact ADAM.

Founding members

 * David Oh (Zero) (leader)
 * Adamska (Ocelot) (informant)
 * John (Big Boss) (icon)
 * Donald Anderson (Sigint) (technician)
 * Dr. Clark (Para-Medic) (scientist)
 * EVA (spy)

Known AIs

 * JD (John Doe, the core AI)
 * GW (George Washington)
 * TJ (Thomas Jefferson)
 * TR (Theodore Roosevelt)
 * AL (Abraham Lincoln)
 * Peace Walker Project AIs
 * GW-Pupa 5000
 * TJ-Chrysalis 6000
 * TR-Cocoon 7000
 * AL-Aurelia 8000
 * BS-Imago

Agents

 * Revolver Ocelot (triple agent)
 * Raiden (unknowingly)
 * Solidus Snake (a.k.a. George Sears)
 * Jim Houseman
 * Richard Ames
 * James Johnson
 * Fatman
 * Rosemary
 * Olga Gurlukovich (forced due to her child being captive)
 * Drebin 893
 * Meryl Silverburgh and Rat Patrol Team 01 (unknowingly)

Cipher agents

 * Pacifica Ocean
 * Vladimir Alexandrovich Zadornov (KGB associate)
 * Kazuhira Miller (business associate)

Behind the scenes
The English "L" sound (as in leaf or mild) does not exist in the Japanese phonetic alphabet, making "La li lu le lo" an impossible utterance in Japanese. Instead, the Japanese have a sound that can be either L-like or R-like depending on its location in a word, with the English "L" being somewhat unattainable. The idea is that the Patriots chose their name to be a phrase that cannot be spoken or written in Japanese. However, since English does have the "L", this concept could not be translated. This idea is also subtly referred to when Emma explains the Patriots attempts at censorship to Raiden and how GW ties in to it, when she mentions that the twenty-six letter alphabet could have originally been thirty and that they removed a few letters.

According to director Hideo Kojima's commentary for Metal Gear Solid 2: Sons of Liberty, the Patriots were conceptualized during Kojima's establishment of the character setting for Solidus, in order to not make Solidus the absolute bad guy. Likewise, in the Grand Game Plan, Kojima stated that he intended the Patriots to be the absolute bad guy, and the American Government, by extension, basing it on a common thread of Hollywood films to make absolute bad guys depending on the times (eg, Native Americans for Westerns, Germany and Japan for post World War II era war films, Russians for Cold War era spy films, Chinese for post Cold War films, terrorists in films made in the 1990s, etc.).

In the Snake Tales story External Gazer, Snake is briefly stuck in a parallel universe and believes that he is Raiden. He and Rose keep getting interrupted while trying to enjoy each other's company. At one point, the "La-li-lu-le-lo" shows up (appearing like the Colonel) on their television set, randomly talking about how to keep toilets clean. They are then joined by two alternate versions, called the "Ta-ti-to-te-to" and "I-ro-ha-ni-ho-he-to", which also give advice. The last version's name refers to Iroha, an old-fashioned Katakana ordering system (the more prevalent ordering is called gojūon). "I ro ha ni ho he to" is the first of seven lines in an Iroha poem that contains each character of the Katakana exactly once, much like the English ABCs song.

Contrary to popular belief, the ask/answer code that Zero supplied to Naked Snake to identify ADAM in Rassvet was not a direct reference to the Patriots, as the Japanese phrases were different (the Japanese word for the Patriots was 愛国者達, whereas the Japanese word for patriot was 愛国者). A commentary by Hideo Kojima also stated that there was no relation between the two.

The ending timeline and post-credits conversation in Metal Gear Solid 3: Snake Eater originally implied that the CIA Director was the founder of the Patriots, after obtaining the Philosophers' Legacy and hoping to revive the organization, alongside Ocelot. However, the DCI's role changed with Metal Gear Solid: Portable Ops, in which Ocelot kills him on the orders of an unknown individual and retrieves the Legacy, to bring about the end of the Philosophers. Metal Gear Solid 4: Guns of the Patriots later identifies the individual as Major Zero.

In Super Smash Bros. Brawl, Snake can contact Colonel Campbell while fighting Luigi, who will make several disparaging remarks towards Snake's opponent. When Snake questions the Colonel's behavior, he begins repeating the phrase "La li lu le lo," implying that he may actually be a Patriot AI.

For unknown reasons, despite Big Boss being stated in Metal Gear Solid 4 as well as implied in Portable Ops to have been one of the founding members of the Patriots, Metal Gear Solid: Ground Zeroes, and to a slightly lesser extent, Peace Walker, had Big Boss referring and reacting to Cipher in a way that implied that he wasn't previously affiliated with the group.