I never changed my index or activity just to clarify. I downloaded mods at first it was a different mod now its AAL. It seems downloading a mod does something to my activities because now I can't play skirmish with normal people and I wanted to do a skirmish with normal dummies and Coalation. I have downloaded new mods without them changing it so it must be something in the AAL file so how do I make it so that I can fight normal skirmish again because I find using normal units on normal units more fun then fighting MPAMs and having explosions ever 2 seconds.

Did you mess with Missions.rte/Activities.ini? As in, delete it? If it's still there, and not lobotomized, simply uncomment the third code block with GABaseDefense in it.
If it is too far gone, consider keeping backups next time and install a fresh copy of Cortex somewhere and copy over Missions.rte/Activities.ini.

I found it in AAL and Emporeans. Apparently (this may just be news to me) you can put a activities.ini in a mod and have it load that instead of the base.rte activities.ini.

Yes. You should probably disable those too, now that I think of it. It used to be that Base.rte/Acitivites.ini overwrote everything but now I remember it's first come first serve, so AAL might be getting in ahead of your Missions.rte. Go into both of those mods and disable the activities by placing // before the line that includes them in the mod's Index.ini, that should fix it if your Missions.rte/Activities.ini is well and good.

It uses the first mod .rte to have an activities file in alphabetical order or, if there are no activities there, it uses the missions.rte one.

I just have a 0.rte with what ever activities loaded.

Problem solved.