I would like to see mission segments that involve defending your ship from a boarding party. Two ways I can think of triggering these events are:
1. After you and your away team have completed their ground mission, your team beams back aboard your ship to find it under siege. And by "your team" I'm including other players that were teamed up with you for the initial ground mission. The team leader's ship is the one that must be protected upon beaming back and you start in the transporter room (as transporter pads are typically kinda small for full squad, simply starting within the transporter room can be inferred as a moment after being beamed back). Your random NPC crew members are fighting back and there are plasma fires in critical areas that must be put out manually, say the engine room, or the bridge, or Sickbay, etc*, and wounded that need treatment. Securing Sickbay would allow the rescue of wounded you come across; securing engineering would allow you to extinguish fires throughout the ship.
If you fall in combat, you and your (npc) team are revived in a secure cargo hold (where other wounded are awaiting treatment) by the emergency medical hologram until you manage to secure Sickbay (unlocked as a new respawn point once secured).
And finally, returning to the bridge where who ever was in charge in your absence informs you that shields are back online and the enemy has cut their losses and fled, (that way the lack of enemy ships when you return to normal flight wont be jarring).
*Note- It is unlikely that any of these locales would share the same deck. Using a turbolift door or a access hatch as click-able transition nodes for your team would act as deck transitions.
2. The above sequence is engaged after a space encounter involved an NPC successfully using the Boarding Party skill against you or your teammate's ship. So once the space encounter is resolved first, then you and your party are given the prompt to transition to the ground mission aboard the affected ship. This allows suffecient time to have passed for the enemy to establish a foothold in your ship.
