So, click the Scenario Battle from the main menu.

From the drop-down list on the left side of the screen (it says "Select Activity" at the top), select Skirmish Defense.

Select a location on the planet to play it on.

Make your base, buy your doodz, play Cortex Command.

EDIT: ♥♥♥♥ me I didn't read your post carefully enough. I just took a peak at those files and I'd imagine you'd maybe have to add ScriptPath = Base.rte/Weather/RunRain.lua to the scenes or something. I'm not scene guy, and not too good at modding files period so if someone with more talent knows, they can probably help.

The weather is WIP and is likely to be removed.