This is the other half of the Ace double book which is paired with Three Worlds of Futurity. I suspect this novel was written for Ace and twined with the story collection when the publisher needed something else to match. As with all of her novels which I've read by Margaret St. Clair, this one is dedicated to her husband Eric, described in the author info as a "well-known writer of children's stories". The same bio piece lists her interests as sports cars, amateur astronomy, cooking, classical antiquity, gem cutting, and mandolin playing. Quite the polymath, she was.
Message from the Eocene begins several billion years in the earth's past. Technically speaking, this would have been the Paleoproterozoic Era. A humanoid creature only known as Tharg is trying to escape the lighting bolts being hurled at him by an unknown source. He's on the surface of the primitive planet Earth on an important mission for the floating city, Synon. He's a member of a specialized group known as "divers" who travel to the dangerous planetary surface in search of valuable minerals needed by the city. Tharg has been entrusted with a container carrying a mysterious book for delivery to the sister city of Gwynor. He's not sure who is tossing the lighting bolts at him, but suspects they are from their enemies, the Veidimi.
When he's captured it turns out the source of the lighting was the Vaeaa, the "half-mythical overlords" who secretly control the third planet from the sun. By now, Tharg has had the chance to open the case holding the book and find out why it's so important. The book is a guide to the secrets of the universe and was sent to Tharg's people by another advanced civilization. But the Vaeaa representatives disapprove of the book. They are strict materialists who feel threatened by it. They give Tharg a psychoactive drug to test out the book's power, then decide to destroy it. Tharg's last effort is to toss the book (in it's container) into an active volcano, where it will be safe until the right life form can find it. His consciousness now separated from his body by the drug, Tharg drifts away from the Vaeaa's in peace.
As Tharg drifts across the ages, he watches his people rise and fall. The Vaeaa overlords vanish too, but not before planting a projector on Pluto designed to prevent any further books from reaching whatever life might arise on Earth. Soon life does arise on the third planet and Tharg decides to contact it when the life forms have reached a level of maturity equal to his former civilization.
His first attempts at contact are rather amusing. His subject is a Quaker family living in New England in the first half of the 19th century. They become convinced their house is haunted from all the strange noises and apparitions Tharg creates while trying to make contact. They leave the house, but Tharg finds himself trapped in it for years. Once he is able to leave, he decides to make a different connection.
The next part of the book concerns a French mining engineer and his wife. She's "sensitive" to psychic phenomena and they're on the island of New Caladonia where he's overseeing a deep mine. One day the mine is filled with strange geometric shapes and the miners refuse to go down to work. The engineer sends his wife down to investigate. After a series of altercations with the locals, the miners, and finally Tharg, the book is uncovered. But it all ends rather disappointingly.
The final section of the book has Tharg trying to find a way to stop the Plutonian projector as he feels another book must be on it's way to the human civilization. Strange sites are seen all over the planet in preparation for the arrival.
Although it seems to be working the same groove as 2001, this book is a lot more fun.