Ambitious concept, and worth continuing to flesh out. It's rough to see what's going on in the browser-scale window, but then going full-screen means I can't see the instructions below the game :,) I couldn't tell which of the colours was mine until I read your description--it was really hard to tell, in terms of responsiveness, what the reaction was to each placed target. It kind of just felt like I was constantly dropping targets all over the map and waiting for something to happen.
It also didn't feel like anything *bad* was happening to challenge me, either? I suspect if two different colours interact maybe that starts something, but they're so far apart that even with it at max speed, none of my guys ended up making contact before I gave up and moved on to read your description instead to see if I was doing something wrong.
The UI options are extremely cluttered in the browser window scale, and it would be best if the game starts with them collapsed, and allowing the player to expand them to see what each one is--this would be a little less overwhelming. Might also be nice to have some tutorialization, or at least a more zoomed-in (gameloop-wise) start to the game so it's a little more clear how your actions as the player impact the game world.
Regardless, a very impressive turnout for four days. Keep working on it!