It took me a minute, but I have a scenario:
Borg nanites or space madness (some force that causes crewpeople to lose control of themselves - doesn't really matter what) have caused the command crew to lose control of the ship while in orbit around a stone age world that they were doing a routine 10 year checkup on. Damage inflicted by the affected crew has caused transporters and engine control to go offline. Command crew has sealed themselves in on the bridge, but don't know how much longer that will remain the case. One shuttle has already launched with affected crew onboard, headed for the planet, and the captain had to order its destruction. More may launch soon, or, if they lose control of the bridge, the whole ship may end up crash landing.
Nothing for it but to send a message to Starfleet letting them know what has happened if you can, and then use the antimatter annihilation self-destruct.