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