The final mini-game in WotA is Warfare, the clash of units in battle. While I have some idea for how many units each faction may get, and how they would move around a map, the narrative scenes leading up to the mini-game, as well as how to create said map, is less clear.
The Infiltration mini-game used set themes in the narrative scenes (setting up and heist and getting away with it, respectively). The other mini-games (Skirmish and Negotiation) use narrative scenes that are pre-written in the text based on the target of the Skirmish or Negotiation. It's difficult to see how Warfare could be reduced to the sorts of narrative scenes present in Infiltration, so I'm leading towards making it work more like Skirmish and Negotiation.
That said, it seems difficult to write narrative scenes, since the Warfare mini-game isn't as constrained. It may be possible to write a variety of example generic scenes in the Warfare chapter, as well as other narrative scenes for each faction in the game.
Finally, there is constructing the map with all the various zones. In Skirmish, this is also largely done ahead of time, although it is possible for the players to add aspects to zones before the fight gets underway. The same tactic may be worthwhile here, although it doesn't seem practical to come up with maps for every single region where a battle could occur. Perhaps a set of general zone maps, which could be modified by adding features in some fashion? The players then may be able to add features to each map as well, in a similar fashion to Skirmish.