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Are the gunships on Mygeeto, Utapau, and Kamino animated? Meaning that they were just kind of moving using the zeroeditor animation function? I've looked at the odfs so I guessing that is what it is because "Pilottype" is set to "None" for pilot so that it could'nt fly away and all the turrets are set to "Self" so that they are basically auto turrets.

Also a thing I find strange is that I have made a side replacement for Mygeeto turning all troopers into Galactic Marines, Baraca, and my own JetTrooper. There are no 501st skins at all. Then while playing campaign mode on Mygeeto, right before you finish the level, you have to return the holocron thing to the gunship. Well I go there and you know how there are troops in the gunship, like in the bubble? Well they have 501st skins. So that would probably imply that they arn't actual soldiers? And that maybe I don't know where I'm really going. I guess post comments and ideas. Whatever

There's a line in the ODF file for the gunship that says 'IsPilotExposed = "1"' or something like that. That makes the trooper appear in the turret. I'm pretty sure that the gunships are animated; the one on Mygeeto at the very end certainly is.

Alright, that makes sense. Thanks for the answer.

If you notice the 501st trooper is in the gunship on kamino when you play as imperials and the opposition are Phase 1 clones...

The gunships that fly around and shoot without any players/bots inside them aren't animated. They just fly by themselves as if there was an AI inside flying them. If you put paths for gunships on any level and put the gunships in that fly by themselves, they'll lift off shortly after spawning in and fly without the need for anyone to board them.
That 501st trooper is the only trooper that appears inside a gunship. He's on the left side. The right side is empty, but both the left and right side work as auto-turrets.

So what you're saying is that the 501st kiddo/pilot there is a part of the .msh? THAT would explain the difference in the name

I don't have a clue what you just said, especially with those sarcastic smilies.
However, in all of the original gunships included in the game, only the self-flying gunship has the one 501st trooper in it. I didn't say that other gunships couldn't have the 501st trooper.

And I said there's several gunships saved if I remember right There's one for Kamino and space and stuffs Gunships really don't fascinate me, so I have no real list of the names it has got

What's your point?

My point? None, really - it just explained why they had more than one file for the gunship