Here is the full list of all 39 Millennia achievements.
Win a game via the Age of the Singularity
Take the timeline into the Age of Visitors.
Take the timeline into the Age of Aether.
Take the timeline into the Age of Monuments.
Win a game via the Age of Harmony.
Take the timeline into the Age of Discovery.
Take the timeline into the Age of Blood.
Win a game via the Age of Conquest.
Win a game by turn 200.
Create a Custom Nation.
Win a game by being the last remaining Nation.
Win a game against at least 3 Master AIs.
Start a Faction.
Take the timeline into the Age of Dystopia.
Take the timeline into the Age of Alchemy.
Start a religion.
Complete an Expedition.
Take the timeline into the Age of Heroes.
Lose a game.
Take the timeline into the Age of Utopia.
Take the timeline into the Age of Ecology.
Take the timeline into the Age of Plague.
Take the timeline into the Age of Intolerance.
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.
Win a game via the Age of Generals.
Win a game via the Age of Departure.
Win a game via the Age of Archangels.
Win a game via the Age of Transcendence.
Win a game by reaching the turn limit.
Reach the Age of Information with only Standard Ages in the timeline.
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.