The player just hijacked a starship.
The cockpit allows the player to take control of the ship and fly it as if it was their own pod, as well as use weapons to attack and destroy other ships. The Hijack mission type requires you to access this part of the ship after subduing all members of the crew, while the Liberation missions allow you to access it at any time to redirect the ship.
This area will usually host the Pilot, a member of the crew that is vital to neutralizing in order to take down the alarm system and turn off the outside heat sensors.