2000s

200X
Late 1999/Early 2000: After losing his faith in humanity, Zero (and possibly Sigint) commissions the development of four neural AIs, and a head AI to inherit the Patriots from him. The four AIs are codenamed GW, TJ, AL and TR and the head AI known as JD. To prepare for the creation of the AIs, the Patriots created and spread a data filter worldwide disguising it as a software fix for the Y2K bug. Liquid Snake ended up joining FOXHOUND shortly after Solid Snake, Roy Campbell, and Master Miller left the unit, becoming its commander not long thereafter. During his tenure as commander, he re-established the codename system with the addition of personal modifiers, as well as reorganized the unit to be a small, hand-picked, elite counterterrorism unit.

Early 2000s: George Sears (a.k.a. Solidus Snake) is appointed as the 43rd President of the United States.

The NIF (National Ignition Facility) was completed and established during this time.

2000
January 1st: Millennium Bug: the Patriots spread a "data filter" worldwide, disguised as a software fix to impede the impact of the flaw in various computer systems.

January 24th: A small group within the U.S. government orchestrates a signal data hacking assault on the NSA facility in Fort Meade, with the assistance of a notorious group of hackers, of which Emma Emmerich is a key member. The facility suffers a total system shutdown for a 72-hour period.

This feat earns Emma invitations to join a host of intelligence agencies worldwide, including the NSA.

The beginning of the Arsenal Gear project: The NSA signal hacking assault led to the decision to shift the NSA data-gathering operations to an isolated location that would be safe from physical attack as well as cyber-terrorism.

June: A joint team of Japanese, American, and European scientist map the human genome.

June: The Eritrean-Ethiopian War ends.

Liquid Snake joins FOXHOUND as the leader of the field combat team.

Ocelot joins FOXHOUND to serve under Liquid Snake.

Trials were conducted on the National Missile Defense program, but they ended in complete failure. At some point, President Sears forced the NMD through and it became successful.

Psycho Mantis left the FBI after delving too deep into a multi-serial killer's mind and became a freelance psychic all over the world.

2001
September 11: Multiple terrorist attacks strike America.

October 7: The War in Afghanistan is commenced as a direct result of the aforementioned terrorist attacks. Sundowner would later become involved in this war, as would Mistral.

2002
Camp X-ray, a black site for housing "enemy combatants," is established at the U.S. naval base at Guatanamo Bay.

Naomi Hunter joins FOXHOUND's medical staff, and begins gene therapy research and experimentation on soldiers.

February 8th: The Algerian Civil War ends.

September: The Third Chadian Civil War ends.

The nuclear weapons disposal facility on Shadow Moses Island is constructed.

Hybrids were outlawed in dogsledding races.

The CIA and other intelligence agencies across the globe uncovered evidence that suggested that Iraq was developing WMDs, which ultimately resulted in the invasion of Iraq a year later.

2003
March 20th: Several nations led by the U.S. launch a multi-lateral strike on Iraq. The United Kingdom-based PMC unit, Praying Mantis, was contracted alongside the U.S. Government to deploy large amounts of their soldiers into the combat zones. Sundowner and Mistral were also involved in this conflict, marking the former's second time in Iraq as well (having earlier participated in the Gulf War). Khamsin would later partake in and end up discharged during this conflict, due to his lack of flexibility and disastrous personality, and underwent mercenary work ever since, eventually using his funds to become a cyborg.

June: The U.S.'s DoD Command and Control Research Program publishes Power to the Edge, proposing battlefield information be shifted to a single Global Information Grid (GIG).

Dr. Clark (a.k.a. Para-Medic) dies in a lab explosion caused by a revived Gray Fox, who manages to escape. Naomi Hunter covers the incident, faking Gray Fox's death, and takes over Dr. Clark's job. This event was planned by EVA and Ocelot as part of their plan to eliminate the three remaining members of the Patriots (the other two being Sigint and Zero).

As of this year, more than 20,000 nuclear warheads exist in the world.

2004
Peter Stillman attempts to disarm a bomb planted in a famous church. He panics and flees the scene, and everyone else in the church and in a nearby playground dies in the explosion. Unable to face the victims' families, he later claims that he lost his leg in the explosion.

Johnny Sasaki joined the military.

An experiment relating to Van der Waals force commenced where they hung a 100 gram object over a 50-millimeter square piece of adhesive tape.

The CIA begins using unmanned aerial vehicles to kill senior al-Qaeda and Taliban leaders in Pakistan's Federally Administered Tribal Areas

Pakistani scientists proliferate nuclear-related technologies overseas.

2005
January: A report was filed where the Next-Generation Special Forces were acting strangely; cunsulting classified information about soldier genes as well as conducting their own gene therapy experiments.

An estimate came out that 50,000 tons of nuclear material was being stored in America alone.

President Sears attempted to reduce the nuclear stockpile, lowering the ceiling with the START III. Simultaneously, Sears tried to negotiate with the Russians to have them agree to a revision of the ABM treaty, since the NMD program violated the current ABM treaty.

Late February: Shadow Moses Incident. The Sons of Big Boss uprising. Master Miller is found assassinated in his home by an unknown assailant. FOXHOUND is "disbanded"; the remaining renegade members are all killed by Solid Snake, with the exception of Decoy Octopus who is killed by the FOXDIE virus created by Naomi Hunter, and Revolver Ocelot, who escapes. The DARPA Chief Donald Anderson dies from torture conducted by Ocelot, who claims it to be an accident, but in truth is because he is Sigint, a member of the Patriots. The President of ArmsTech Kenneth Baker is killed by the FOXDIE virus, as well as the majority of the Genome Army. Solid Snake meets Hal Emmerich (Otacon) and Meryl Silverburgh for the first time. Gray Fox, with his new exoskeleton, battles Snake and is defeated. He is eventually killed by Liquid Snake. Solid Snake destroys Metal Gear REX. Liquid Snake is eventually killed by FOXDIE. Snake leaves with Meryl in an attempt to start a new life.

Naomi is placed into a high security prison. Three weeks later, she is broken out by Liquid Ocelot. Because both the U.S. Government and Nastasha Romanenko (the latter after hearing from outside sources about the breakout) believed that Solid Snake was the one who broke Naomi out, the military also added Snake's supposed involvement in her escape to his rap sheet.

Nastasha Romanenko publishes her best-selling book In the Darkness of Shadow Moses: The Unofficial Truth, in order to expose the truth behind the incident, although it ended up being heavily abridged.

Revolver Ocelot sells the data for Metal Gear REX on the black market. Soon, every nation, military outfit and DotCom owns a pirated version of the weapon. Ocelot also gained in return enough money for him to buy a decent-sized nation, which was suspected to have been used for a project.

George Sears (Solidus Snake) "resigns" as President. He is succeeded by James Johnson.

Emma Emmerich joins the NSA in exchange for information regarding her brother Hal Emmerich, who had been involved in the Shadow Moses Incident.

Jim Houseman allegedly committed suicide due to a nervous breakdown relating to his job, although it is suspected that he was actually assassinated for failing to take the fall for the Patriots' plan.

Simultaneous terrorist bombing cases take place in London, Egypt, and France.

Late 2005/Early 2006
In Lyon, France, Ocelot has Liquid Snake's arm grafted in place of the one Gray Fox cut off at Shadow Moses as part of a plot to rescue Big Boss's remains and free him.

2006
Solid Snake and Otacon found Philanthropy, in order to put a stop to the construction of Metal Gear derivatives. Nastasha Romanenko donates half her profits from her book to their cause.

The Boeing X-50 Dragonfly ended up cancelled due to flaws in the transition mode between winged flight mode and rotor mode.

July 16th: The Global Initiative to Combat Nuclear Terrorism created by US and Russia.

2006-2007
Jack (Raiden) undergoes VR training as part of the U.S. Army's Force XXI trials.

2007
The Global Financial Crisis begins.

January 20th: Jack (Raiden) leaves the Force XXI, with his profile within the group being edited for the last time.

April 30th: Jack (Raiden) and Rosemary meet each other for the first time.

May: Rose and Jack (Raiden) become reacquainted upon discovering that they work at the same military base; Gary McGolden, a journalist for MEGASURPRISE magazine, is given an optical disc containing a copy of In the Darkness of Shadow Moses: The Unofficial Truth.

Olga Gurlukovich becomes pregnant with Sunny.

June 24th: Gary McGolden supposedly travels to Shadow Moses Island to discover the truth about the 2005 incident, but is captured by agents of the Patriots, resulting in his rescue by an unknown "invisible" savior. Later, he publishes his article: The Shocking Conspiracy Behind Shadow Moses. As a result, In the Darkness of Shadow Moses: The Unofficial Truth is published in its original, unabridged form.

August: Three "special weapons observation remote reconnaissance direct action system" (SWORDS) are deployed in Iraq, marking the first unmanned, armed robots in a warzone.

August 8th: Tanker Incident. Solid Snake infiltrates the USS Discovery (tanker) in order to take photographs of Metal Gear RAY, to leak onto the internet. Snake meets Olga Gurlukovich for the first time. Ocelot then hijacks RAY, murders Scott Dolph and Sergei Gurlukovich, sinks the tanker and is then taken over for the first time by the personality of Liquid Snake, thus beginning his transformation into Liquid Ocelot. Philanthropy is blamed for the incident and goes underground, faking Snake's death.

Dead Cell leader Colonel Jackson is arrested for allegedly misappropriating government funding and incarcerated in Leavenworth. He was actually framed by the Patriots.

Construction on the Big Shell offshore decontamination facility begins in Manhattan Bay.

Emma Emmerich leaves the NSA. She is recruited by the Patriots to begin work on GW.

2008
The FDA of America declares food from cloned animals safe practice.

February: Olga Gurlukovich gives birth to Sunny, who is kidnapped by the Patriots.

September: The Montreux Document was ratified, which allowed for some obligations in signature countries regarding private militaries.

November: The liquidation of Dead Cell: Dead Cell is caught in a surprise attack, losing two of its key members (Chinaman and Old Boy). Only Fatman, Fortune and Vamp survive.

James Johnson was re-elected as President, officially due to the policies he made, although it was largely due to the Patriots' manipulations.

The President of the United States publicly pledges to close the detention facility at Guatanamo Bay.

Sundowner retired from official military service, and began working as a mercenary for various PMCs.

2009
January: Scientists succeed in cloning the first extinct species, the Pyrenean Ibex.

February: The Tea Party Movement was formed.

April 29th: Big Shell Incident. The Sons of Liberty uprising. Raiden and Solid Snake infiltrate the Big Shell separately. Raiden is unknowingly used as a guinea pig in the Patriots' S3 Plan in order to provide complex data for one of their AI's (GW). Raiden is variously assisted and opposed by both Snake and the new Cyborg Ninja (Olga Gurlukovich). The incident results in the deaths of Fatman, Emma Emmerich, Olga, Richard Ames, Peter Stillman, every member of SEAL Team 10, and the 44th President of the USA, James Johnson. Vamp is also "killed" for the 2nd, 3rd and 4th time, all at the hands of Raiden.

April 30th: Arsenal Gear emerges. Fortune is murdered by Revolver Ocelot who becomes Liquid Ocelot once more, then proceeds to escape in Metal Gear RAY. Arsenal Gear crashes into Manhattan, stopping at Federal Hall. Solidus Snake dies after being defeated by Raiden. Otacon discovers that the original Wisemen's Committee has been dead for almost 100 years, and that one member was also one of the top financial backers of Philanthropy.

Liquid Ocelot retrieves GW from Arsenal Gear.

Revolver Ocelot has Liquid Snake's arm removed from his body because the arm caused an imbalance to Ocelot's psyche in the presence of Solid Snake during the Tanker and Big Shell Incidents. It is replaced with a cybernetic prosthetic.

June 23rd: The United States Secretary of Defense establishes Cyber Command, the Armed Forces Branch of cyberspace.

Behind the scenes
The timeline featured on the Metal Gear Solid The Legacy Collection official website mentions President Barack Obama's 2009 speech about "A World without Nuclear Weapons" in Prague, Czech Republic. However, this conflicts with the Metal Gear chronology in that the President during this time is actually the fictional James Johnson.