In Assassin's Creed Odyssey, whether to destroy the stone or send it back can be referenced as follows:
It is best not to destroy the stone in Birds and Bees in Odyssey, because it is related to the subsequent plot.
If you choose to follow Neocris's plan, you'll need to put the Power Stone into the launcher. This will grant you additional Ys Knowledge points.
If you choose to listen to the thief scientist's advice, you will also gain a small amount of Ys knowledge points. Regardless of the choice, the thread will close smoothly.