This is a guide to the timeline of events in Tales of Eternia, including how the side materials fit into the story chronology and how they diverge from the game story. Every story-related event is described here, so be careful if you're sensitive to spoilers.
I only have dates for historical events and the year the story begins in-universe. It's unknown how much time elapses from start to end, or how long each event takes.

Historical chronology:

B.S. (Before Seyfert) 6000 (10,000 years ago)--Nereid creates Baten Kaitos

B.S.4000 (8,000 years ago)--Seyfert creates material universe

S.E. (Seyfert Era) 1 (3,800 years ago)--Formation of Melnics planetary union, and beginning of Melnics Era

S.E.1500 (2,300 years ago)--Start of Aurora War

S.E.1600 (2,200 years ago)--Seyfert seals off Celestia and Inferia with Seyfert Ring

I.R. (Inferia Rule) 1 (198 years ago)--Founding of Kingdom of Inferia

I.R.198--Present year in Tales of Eternia

Story chronology:

G: Prelude in Celestia. Meredy departs for Inferia on the craymelcraft.

D: Prelude in Inferia. Ras massacres Nereidite cultists in Barole. The Seyfert Key begins to emit light toward a particular direction. (CD1:1,2; CD2:1)

G01-02-03, D: Racheans, the Village at the End of the Earth. Meredy crashes into the forest nearby, and is discovered by Reid and Farah. Hyades attacks the village in search of Meredy, but is repelled by Reid and Farah. Reid, Farah, and Meredy depart for Mintz. (CD1:3,4,5)

G04-05: Regulus Hall. Trip down Racheans River to Mintz.

G06-07-08-09: University of Mintz. Reid, Farah, and Meredy ask for Keele's whereabouts and depart for the university observatory.
-D: University of Mintz. Keele's thesis is rejected by Prof. Carlisle. Reid and Farah track Keele down and ask him to join them. (CD1:6,7)

G10, D: Nostos Cave. (CD1:8)

G11-12-13, D: Morle. (CD1:9,10,11)

G14: Stream of the Water Craymels.

G15: The Forest of Temptation.

G16-17, D: Inferia City. (CD1:12)

G18-19: Barole.

G20: Cavern of the Wind Craymels.

G21: Gorge of the Fire Craymels.

G22-23: Mt. Farose.

G24: Cape Fortress.

G25-26-27-28: Imen, the Town where Craymels Dwell.

G29-30-31: Luishka.

G32: Abandoned Mine of the Earth Craymels.

G33-34-35: Chat's Hut.

G36: The Van Eltia.

G37: Port Town of Peyruti

G38: Mountain of the Ice Craymels.

G39: Port Town of Peyruti 2.

G40: The Van Eltia 2.

G41: Imen, the Town where Craymels Dwell 2.

G42: Tinnsia, the Town of Craftsmen.

G43: The Ruins of the Lightning Craymels.

G44: Tinnsia, the Town of Craftsmen 2.

G45: Balir Castle.

G46: The Ruined Village of Luishka.

G47: Tinnsia, the Town of Craftsmen 3.

G48: Seyfert Shrine.

G49: Chat's Hut 2.

G50: Aifread's Grotto.

G51: The Van Eltia 3.

G-EX: Jini, the Town of Delight.

G-EX: The Cavern of Darkness.

G52: Celesea Hideouts 1-5.

G53: Aifread's Platform--The Bridge of Expedition--Relay Base.

G54: The Van Eltia.

G-EX: Aifread's Tomb.

G-EX: The Sunken Ship.

G-EX: The Farose Church Basement.

G-EX: Insea Hideouts 1-4.

G55: Seyfert Garden.

G56: The Royal Capital of Inferia.

G57: Port of Inferia.

G58: Seyfert Observatory.

G59: The Van Eltia.

G60: Racheans, the Village at the End of the Earth.

G61: Tinnsia, the Town of Craftsmen.

G62: Balir Castle.

G63: Tinnsia, The Town of Craftsmen.

G64: Regulus Knoll.

G65: Racheans, the Village at the End of the Earth.

G66: Balir Castle.

G67: Shizel Castle.

G-EX: The Van Eltia.

G-EX: Craymel Hot Springs.

G-EX: The Hamlet of the Catpeople.

G-EX: The Glimmering Spire.

G-EX: Nereid's Labyrinth.