A Bunker has two two functions:

Active function allows you to hide your fleet from enemy attacks. The bunker hangar capacity depends on its level and the Event Horizon technology. A fleet hidden in the bunker is not displayed in the ship dispatch window.

The passive function allows to save some of the resources from plundering if your defense was unsuccessful. You do not need to add resources to the bunker — they are saved automatically. The number of saved resources increases with the bunker level and with the Underground Cavern technology.