This is a difficult one, as we don't know the reason that the pilot isn't going on the "away missions".
Answering the main question:
Pirates/local big bad/aliens/space whales/asteroids attacking
If you don't mind it being a bit dangerous, have the pilot fight off or defend against lots of small enemies whilst the party are planetside.
I'm assuming the reason that the pilot isn't going on missions is because he's particularly fragile. Have him get a drone or robot body to go down in instead. Either something along the lines of a mobile robot body similar to Mass Effect's EDE (using pre-scream tech) or something similar to 40K's Tau mobile gun drones. This allows your pilot to be "Safe" in space whilst his robot body gets shot at. Just don't make it too heavy so it can be recovered if it gets particularly shot up!
Similarly, encourage the pilot to come along on the away missions. If he's worried about fragility, as a pilot he should have some exo suit training — have one of these at the appropriate level turn up for sale or as loot. Should he need to be shipside for story reasons, have it break down unexpectedly, or have some weird atmospheric/localised special disturbance/[insert thingy here] effects.
Assuming your pilot isn't going on the missions to look after the ship(s) have him decoding signals or asking questions in ports etc. He can be on standby in a pub next to the terminal If needed.
Have the players go into deep space, boarding ships, derelicts and installations. The pilot can do much more here, defending the derelict from space junk/fighters/unicorns whilst the rest of the party do their thing. This is potentially a good stop-gap whilst you discuss the next part of this answer with the player.
Ask the bigger question of "Why isn't the player staying with the group":
If the player isn't happy to go on away missions — why is this? Speak to him one on one to find out if he's after more of a space-based game, and offer this up for discussion with the rest of the party.
Has he painted himself into a corner with his character build? Give him some gear to help him do more planetside (telepresence, exo suit, exoskeleton). Heck, you could even have him involved in an accident (with his permission of course) where as part of it he gets some free prosthetics. Make sure to clear this with the party too!
Does the party need a shipside presence? - get them an AI!.
Do you want the player shipside instead of on the missions?
If so, examine it with the player. If they don't want the character on away missions as well, explore the options in the other answers and any others other users come up with. If he does and you don't, try and see it their way and go with what the players want. There are always ways of convincing the party to split when needed, but (IMO) its better to have the party acting as one big group.