It is impossible to have an universal dating system in Warhammer 40,000 universe. Different planets may experience passing of time differently than others. Some galactic events have flung people and things forwards or backwards in time. Additionally, certain locations exist outside the physical laws and thus outside of time. Some races don't probably even have a concept of time like the tyranids. Even the Imperium of Man doesn't have a single dating system.

But the most widespread dating system is the Imperial Dating System. This is mainly because Warhammer is viewed through the eyes of the Imperium, humans are currently most widespread race that wants to record dates and the Imperial Dating System is closest to our real life dating system.

Imperial Dating System:

A.BBB.CCC.DDD
|  |   |   >  millennium
|  |   > year
|  > year fraction
> check number

• The check number tells how accurate the time is between 0 (known to be accurate) and 9 (a wild guess)
• Year fraction, a year divided to 1000 parts, approx 8 h 45 min each
• Year is year number between 0 and 999 in the given millennium
• Millennium is denoted with an M-prefix e.g., M21 would be 20,000–20,999

022.M3  ==   2022
999.M41 == 40,999

Timeline:

• -M60,000
  • The War in Heaven
  • The Old Ones vs. Necrontyr
  • C'tan ally with Necrontyr
  • C'tan eat the life energy of Necrontyr
  • Necrontyr become Necron
  • The Old Ones create many races e.g., Eldar and pre-Orks
  • The Old Ones are still defeated
  • Necron fight and enslave their C'tan masters
  • Eldar are winning the war against weakened Necrons
  • Necrons enter 60-million-year hibernation to let Eldar power fade
  • Eldar became the dominant species... for the time being
• -M8
  • The being that will be called The Emperor is born
• 500.M1 - 500.M2
  • The European Middle Ages
  • Khorne is born from the ongoing warfare
  • Tseech is born from the emerging political scheming
  • Nurgle is born from the rampaging diseases
• M1 - M15
  • Age of Terra
  • Sol System is colonized by humans, mainly driven by corporations
• M15 - M25
  • Age of Technology
  • The first galactic conquest by humans
  • Navigators and the earliest use of the Warp for interstellar space travel
  • Astropaths and establishment of interstellar communication
  • The highest point of human technology
  • Ended with a civil war with the Men of Iron artificial intelligence
• M25 - M30
  • Age of Strife
  • Humans lose all their artificial intelligence-based technology
  • Human colonies become isolated from one another because the loss of technology
  • Humans become afraid of technology
• M30
  • Fall of the Aeldari: Slaneesh is born, creating The Eye of Terror
  • The Emperor takes a more active role in the human society
  • Unification Wars around 900.M29 - 500.M30
  • The Imperium of Man is formed from the unified Terra
  • The Treaty of Mars is signed
• 798.M30 - 006.M31
  • Great Crusade to gather lost human civilizations
• 006.M31
  • The highest point of galactic human civilization
  • And then the Horus Heresy happens
  • Emperor's body dies and mind becomes trapped
• M31 - M41
  • Age of the Imperium

The Emperor

For all of human history, there has always been exceptional beings with clairvoyance and other mysterious powers. Depending on the time period and culture, they have been called shamans, druids, witches, warlocks, wizards, etc.

In the 41st millennium, they are called psykers.

Around 8,000 B.C. many separate shamans gain visions of the future of humanity. And the future is not looking good. These awoken psykers telepathically convince other psykers to join a mass-ritualistic-poison-suicide so their souls can be freed and later reincarnated into a single super-being that can steer humanity from the path of sure destruction.

A year later, an immortal child was born in what is now modern-day Turkey. This child will become known as The Emperor of Mankind. He lives for 38,000 years in the shadows, gradually gaining wisdom of his past lives, learning by observing and nudging humanity towards progress.

Around 30,000 A.C. the Emperor takes a more active role in leading humans to a more prosperous future, uniting all humans on Terra and forming the Imperium of Man. Most of the humanity is still way beyond contact, all across the Milky Way.

The Emperor begins his Great Crusade to gather all the long-lost human colonies under the same flag, the Imperium of Man. All colonies join; either willingly or by force.

The Emperor forbids all religion and teaches the Imperial Truth for around 1,000 years. Imperial Truth is an ideology that promotes reason, science and progress; while denouncing superstition and prejudice.

Emperor's body dies on 006.M30 on Holy Terra as the result of Horus Heresy, becoming a flesh prison of his immortal mind. Each day, 1,000 human psykers are sacrificed to sustain what little is left of the Emperor.

And then humans start to worship the Emperor as an all-mighty-god, an exact opposite of his teachings about the Imperial Truth.