Here is the full list of all 39 Millennia achievements.
Reveal Glitch #4 - Darkness.
Reveal Glitch #3 - Nonlinear.
Reveal Glitch #2 - Purpose.
Take the timeline into the Age of Plague.
Reveal Glitch #1 - Calibration.
Win a game via the Age of Generals.
Win a game via the Age of the Singularity
Reach the Age of Information with only Standard Ages in the timeline.
Take the timeline into the Age of Dystopia.
Take the timeline into the Age of Discovery.
Win a game via the Age of Conquest.
Take the timeline into the Age of Ecology.
Take the timeline into the Age of Ignorance.
Take the timeline into the Age of Monuments.
Take the timeline into the Age of Visitors.
Take the timeline into the Age of Aether.
Take the timeline into the Age of Intolerance.
Win a game by being the last remaining Nation.
Win a game by turn 200.
Take the timeline into the Age of Utopia.
Win a game via the Age of Transcendence.
Take the timeline into the Age of Alchemy.
Take the timeline into the Age of Blood.
Win a game via the Age of Archangels.
Start a Faction.
Lose a game.
Win a game via the Age of Harmony.
Win a game via the Age of Departure.
Complete an Expedition.
Start a religion.
Take the timeline into the Age of Heroes.
Create a Custom Nation.
Take the timeline into the Age of Heresy.
Take the timeline into the Age of Old Ones.
Win a game by reaching the turn limit.
Win a game against at least 3 Master AIs.
Reveal Glitch #5 - Truth.
Reveal Glitch #6 - Project ATLAS.
Win a game via Project ATLAS.