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