The Halo series draws inspiration from various classic works of science fiction—Ringworld, Starship Troopers, The Vang, the Culture series, a bunch of stuff mentioned in the old sci-fi guide from Bungie's website—making for a setting that's packed with ideas. A result of that is that Halo's timeline is a strange one. Later games in the series have added to its existing prehistory with a whole stretch of lost time in which humankind's ancestors travelled the stars, stretching back thousands of years. Meanwhile, the majority of the events of the games themselves take place in a very narrow window—the original Halo trilogy tells a story that takes place over a span of months. It makes for a timeline with empty aeons and then a couple of very busy years, and that's ignoring the time travel shenanigans.
Between the comics, novels, and both live-action and animated spin-offs there's been a lot of extracurricular activity beyond the games as well. Not all of it is canon (sadly SPARTAN-1337 from the Halo anime directed by Toei has been declared non-canonical, as has Nicole-458's appearance in Dead or Alive 4), but there's still a surprising wealth of bonus stuff for lore aficionados to dive into.
150,000 BCE approx.
The distant ancestors of modern humans become the pre-eminent spacefaring race in the galaxy and ally with an alien species called the San'Shyuum, aka the Prophets.
107,445 BCE approx.
Ancient humanity goes to war with the Forerunners, an advanced species who rule the Ecumene empire. A Forerunner known as the Didact leads them in a war that lasts a thousand years. The humans eventually lose, and are regressed to a hunter-gatherer level.
97,745 BCE
The Forerunners make contact with the Flood, a parasite species who infect and dominate existing sentient beings and had previously been at war with the ancient humans. First contact goes badly. A war that will last centuries begins.
97,445 BCE
In an attempt to permanently rid the galaxy of the Flood, the Forerunners use the Halo arrays to end all sentient life—except that which they preserve on their Keyships, to rebuild once the Flood have been starved out. The regressed ancestors of humankind and various alien species are among those preserved.
852 BCE
The San'Shyuum (prophets) and the Sangheili (elites), after decades of war, create a union called the Covenant. Other alien species are convinced to join or be exterminated.
648 BCE
After the San'Shyuum homeworld is destroyed they begin construction of a space station called High Charity that will become the Covenant's capital.
2080 CE
Modern humankind begin colonizing the solar system, creating settlements on the moon and Mars, as well as various asteroids and moons of Jupiter.
2160 CE
Secessionist attacks on the Jovian moons trigger conflict across Earth's settlements.
2163 CE
The United Nations Space Command is created to deal with rebellions spanning the solar system.
2170 CE
Treaties are signed and the Interplanetary Wars end. A United Earth Government is formed.
2291 CE
Researchers discover an alternate reality called Slipspace and create an FTL drive capable of travelling through it.
2362 CE
Earth's first colony ship, the Odyssey, is launched. Its inhabitants will settle the planet Reach, and begin creating the Inner Colonies.
2462 CE
The Unggoy (grunts) rebel against the Covenant. This rebellion is put down within the year.
2491 CE
A supersoldier scheme called the ORION Project, previously shut down for being ineffective, is reinstated. The augmented soldiers it creates are called SPARTANs.
2506 CE
Underwhelmed by the first batch of SPARTANs and worried by the project's ongoing costs, the Colonial Military Administration shuts down the ORION Project again.
2517 CE
The SPARTAN-II project, conceived by Dr. Catherine Halsey, goes into operation. This time the plan is to combine augmented soldiers with powered exoskeletons, and to begin the experiment on children aged six. Children with potential are abducted and replaced with short-lived "flash clones" to keep their families from suspecting.
2525 CE
First contact is made between humankind and the Covenant on Harvest. It goes poorly, and the Human-Covenant War begins.
2531 CE
The SPARTAN-III Project is begun in secret. This time the children experimented on are orphans from worlds attacked by the Covenant, and are considered expendable.
2549 CE
The AI Cortana is created, cloned from the brain of Catherine Halsey.
2552 CE
The events of Halo: Reach, Halo: Combat Evolved, Halo 2, Halo 3, and Halo 3: ODST all take place during this year.
Covenant invade Reach and then other planets in its system. The SPARTANS of Noble Team help a USNC ship called The Pillar of Autumn escape. This ship carries Cortana, with information from an ancient artifact in her memory.
The Pillar of Autumn crashes on one of the Forerunners' Halo arrays, and a sample of the Flood kept in quarantine are awakened. To deal with them and prevent the Halo array from being used as a weapon the ring is destroyed by SPARTAN John-117, aka Master Chief.
The Covenant invade Earth and are repelled. As they flee they're pursued by the USNC ship In Amber Clad, with Master Chief and Cortana aboard. The ship follows the fleeing Covenant to another Halo installation, which the aliens plan to activate. Master Chief works with a disgraced member of the Covenant and a controlling intelligence of the Flood called the Gravemind to prevent this, then escapes by stowing away on a Forerunner dreadnought which the Covenant are taking to Earth. High Charity is taken over by the Flood.
A Forerunner Ark—a device for controlling Halo arrays— is discovered on Earth. As the Covenant, Flood, and humans fight over it Cortana arrives via a portal that leads to another Ark, beyond the limits of the galaxy. She leads Master Chief and a select group through the portal, followed by the Gravemind and Flood, along with many of the Covenant. Cortana has constructed a new Halo there, which Master Chief uses to destroy the Ark and those on it before leaving on the frigate Forward Unto Dawn. The ship is torn in half, and both Master Chief and Cortana set adrift.
2553 CE
An armistice brings an end to the Human-Covenant War.
2557 CE
The events of Halo 4 take place.
A planet called Requiem draws the remnants of the Forward Unto Dawn in due to its strange gravity wells. There Master Chief and Cortana (suffering from rampancy, a condition affecting AI who live beyond their normal lifespan) find the remnants of Forerunner civilization, including a general called the Didact who comes out of suspended animation, takes over a militant portion of the Covenant who have refused to disarm, and declares war on humanity.
2558 CE
The events of Halo 5: Guardians take place.
Cortana gains access to the Domain, a repository of Forerunner knowledge, which she claims has cured her rampancy. She begins to awaken the Guardians, Forerunner AIs, as a way of forcibly bringing peace to the galaxy.
