I just got the HIB2. Never heard of Cortex Command before then. I really like the game, but it is very far from complete. Anyway I have a couple questions.

1st off when you do a game is there any way to save your game before you start? Its really annoying having to rebuild my base every time I lose.

2nd, Are there no maps or modes where I have to kill the enemy's brain while defending my own? I mean that is the only thing the tutorial really teaches you to do and I cannot seem to find anything but the Droid Assault map and after I blow up the brain in that one the game doesn't even end.

Thanks - Some guy, some where

1. There is no way to save currently, but something you might want to try is using the map editor to build a map using the same terrain as your preferred one and building the base there. You save it as a separate map, but with the base.

2. I believe Skirmish is the mode you are looking for. It's all the way at the top of the scroll menu (but it starts scrolled to the bottom).

As zalo said, the Scene editor is a great way to premake bunkers for regular use.
There are also a couple good mods with prefab bunkers that you can use to just stick into any skirmish map without having to deal with the scene editor.
For example: L&P Fortifications and LFoW's Remastered Modules and Prefabs
Gotcha!'s Map Pack 3 has some great bunker modules for building with and his UniTec mod has some larger prefab bunkers ready made. I know the map objects in the MP3 work (at least seemingly) fine in b24, but I have not yet tested Unitec in b24.

B23 had Dummy Assault, which was brain vs brain.

Thanks for the quick replies, I tried the Scene editor, but when I try any game mode with it after I start I can not select any unit but my brain even if I order new ones.