“Batten down the hatches” is a traditional naval order to securely cover the openings or hatches to the hold on the deck of a sailing ship.
Batten is the key word and comes from the same root as the French word baton, like the one used by an orchestra conductor or in a relay race.
A batten is a strip of wood, which in this case was used to nail down a tarpaulin over the ship’s hatches during a storm.