Battle Academy was designed from day one to be both easy to mod, and to allow modders to do almost anything they wanted. So you can start by using the ingame editor to build missions, set simple objectives for the AI, and use the editor plugins to set up Victory Point missions, or randomise the AI forces. But go a little further and you can begin building customised mission behaviours using the simple scripting that drives everything from the missions, to the unit behaviours, to defining all the orders which you can give to any of your units.
You can see the results of this in the various user content available both ingame, and on the Slitherine game forums.
You can begin by simply creating new maps for the existing game. This can all be done in-game, using the Editor option on the main menu (note: the editor is not available on the iPad version of the game).
But suppose you want to change the stats on a unit, or even add a new ability or order it can perform. Or change the way that the game simulates armour? Or even add in new 3D unit models? All that - and more - can be done without needing any special tools or skills.