I'm using the EVO plugin for EV Nova, and everything's been going great. My game froze so I restarted it, and instead of flying my Crescent Warship I'm in a shuttle with three neutron turrets. I just destroyed the Voinian Dreadnaught and this happened when I landed back on Bakka, it gave me a warning that I"m using a plugin that doesn't work and it may cause some "odd behavior"...such as me wasting several hours of gameplay and 15.00Million credits 
Any ideas as to why this happened? I have no plugins in my folder.
Need help
Wait wait wait, did this happen in-game or when you exited and reloaded you pilot? Or is it neither of those? I'm trying to get a better understanding of what happened here, the way you explained it is a little vague.
If you take out a plug-in that changed an important aspect, it often glitches.
See: Equipping some stuff from PlugPack and then removing it before the next game
Messes up your pilot file something fierce, which is why I normally "back up" some of my favorite pilots when I am doing a storyline (I always delete them in the end, but that is because I love starting from scratch)
Well I was in game, I finished the Dreadnaught mission, left Alpha station and I boarded a Voinian Frigate and boom, it froze mid-game. I did however previously (sometime earlier, but I had restarted the game several times beforehand) remove the plugin that darthkev posted on one of my previous posts the universal money plugin.
That shouldn't have an effect, it is an event that just grants normal cash. No special outfits or anything.
True, my plug-in shouldn't cause a problem. However, I've had problems boarding Voinian Frigates in the past, too. Both in the original game and with the 'official' port of EVO. However, such problems stopped when I started using Guy's port.
So which port are you using? If you are using Guy's port, then we need to look for some other cause. However, if you're using the 'official' port, then that could be the cause.
You don't know? Oy vey... alright, go to this site and download the EVO port there. Feel free to download the EVC port, too, if you wanna play it. Let us know if that fixes your problem.
And another quick question, When I downloaded EV Nova, there was no folder with the pilots/ plugins in it, why?
That's because EVN makes that folder when you first start it up. It's wasn't there yet because you hadn't run EVN yet.
Where are you looking for the folder? It should be in the pathway '~/Library/Application Support/EV Nova/' where '~' is your home folder. Also, that's if you're on a Mac. I do not know the pathway for PCs.
Yeah, I'm on a mac. I can see where it is when I open up the game, but I can't put in any plugin files or access it out of the game for some reason.
Yeah, all that shows up is the actual game and I went to show package contents and such and didn't see it, where's the application support located at?
Wait a second. Have you been looking at EVN's package contents all this time? No wonder you can't find them, the Pilots and Plug-Ins folders aren't in there. Click on the Finder icon in your dock. When the window pops up go into the Library folder, and you should be able to find your way from there using the directions I provided in one of my previous posts.
Ohh well that would explain it, thanks. Oh and a random question, any idea on where to get the starting mission for the Igadzra?