You're definitely thinking on the right track. The problem you state is just what a relational database is for.
Entities as I see them:
user
mission
plane
crewman
I like to use singular names for tables: plane, not planeS. Old habit.
I'm calling one entity 'crewman'...individual records about individual people.
There's a nice top 1 to many relationship:
1 user has 1 to n missions, each mission has 1 to n planes, each plane has 1 to n crewmen.
You probably, however need some intermediate tables:
Each mission has MissionStatus: the status of planes involved at any given time, changing with changes in play.
Mission>MissionStatus>Planes
You'll actually need to create a table between them:
MissionGroupPlanes
Mission>MissionStatus>MissionStatusPlanes>Planes
Can you see how this would work?
You create a mission and the missionstatus record
missionid=222
missionstatusid=9292
status='startup'
As things change
missionid=222
missionstatusid=9293
status='takeoff'
etc
for each plane at each point in the mission status, a missionstatusplane record:
missionstatusid=9293
planeid=888
missionstatusid=9293
planeid=928
connecting to plane ids 888 and 928 respectively:
SELECT name
FROM plane
WHERE missionid=222
AND status='takeoff'
AND mission.statusid=missionstatusplane.missionsionstatusid
AND mission.id=missionstatus.missionid
AND missionstatus.planeid=plane.id
The first 2 wheres (222, 'takeoff') are the ones where you look for info.
The rest are how to join the tables together to prevent duplicate rows.
Similar for the crew
missionStatusPlaneCrewRevision
missionstatusid=929
planeid=888
Revisionid = 123
CrewRevisionCrewman
revisionid=123
crewman=1
crewmanstatus='alive'
which would relate to crewman records,
etc.
It's a pleasantly complex datastructure, with plenty of opportunities for establishing rules for creating and updating records.
Don't freakout that it seems complex at first glance. Most relational dbs appear that way, but once you get used to the concepts, it is SO much simpler to manage a many-tabled relational database than it is to try and cope with 'simpler' datastructures preferred by novices.