I'm missing a file in my base.rte folder. When I try to run cortex command, it gets halfway through my mods and then realises the missing file. Can anyone help?

Sure, if you tell us these important points of data, so that we can make a beautiful line.
1. What error, verbatim, are you getting? Also, what file is missing?
2. What version of CC are you using? This includes Mac or PC version and the b number, as in b21 or b22 or whatever. For instance, I use PC b22.
3. Did you do any of the following: mod your base.rte, edit any files in your base.rte, install any mods into base.rte or edit/make a scene in the scene editor?

If you give us all that, we should be able to help you. Sometimes these errors just happen and there is no way to fix it, but the above will let us fix it if it is fixable.

It says that it failed to load datafile object with following path and name: base.rte/actors/coalition/torsoB.
I think i'm using the latest build for PC. Is there any way to check?
It was an ingame error. I was using a mod and suddenly, BOOM. Explosion and it gave me an error message. How can an explosion ingame tear a hole in the fabric of space-time and end up shredding a file?

You probably are using PC b22 then. What mod was it, and did you try uninstalling and reinstalling? I haven't heard of that happening, but then again CC has been known to eat settings.ini, so why not a bmp too?
If you don't want to do a full uninstall/reinstall, you can try repairing that file with this copy that definitely works on mine. Just find where it should go and paste this over it.

I think the whole coalition file is missing from base.rte, and it's trying to load TorsoB first. There is no coalition file in base.rte/actors.

I think you may have placed torso.bmp in the wrong place, have you tried putting in Coalition.rte? As it is also a game file...

I haven't touched any files in the cortex command folder except for Scenes.ini to add an entry so I could access a mapset.

So what is the exact error message returned and what mods are installed?

Have you got Capnbub's crobos installed?

That must be some old mod your using becorse there shoud not be coalition stuff in base.rte if I'm correct. So, to use that mod move the TorsoB.bmp file in to the path that the error message says. If there don't exist that kind of path then create it. Simple, I guess.

I cut my losses and put all the files I could find (All the coalition body files (arms, legs, that sort of stuff)) into a newly crated folder titled "Coalition". If it screws up again, I'll uninstall, find the registration code and reinstall.

Edit: Whatever it needed, it's working now.

That would suggest some of the files were in use or some such...