The Docking Bay is where you start the game and where you go back when you run out of Ammo or run low on Shields. Each player brings 2 ships to the fight and can switch between the two of them as long as they keep either from being wrecked. Should one be wrecked, the ship will be replaced with a Drone. The Drone simply has a cooldown before being usable again when wrecked.
On top of this, any player can lend his ships to allies by clicking on "Share" while docked or by accepting share request by pushing F5. This allows to further continue switching between ships even if you got one wrecked early in the game. Players may also push F6 to decline sharing.
The Docking Bay is also used to gather information on the state of the match. From this position, you can look at both carrier ships' parts by pressing Alt and inform your teamates via the Chat or Voice Commands of which parts are damaged.