Right, save, and quit Darwinia entirely. You CAN test your level now if you like, but I wouldn't bother. You'll only have to do it again in a minute. Hopefully you didn't close your explorer/whatever program with your mod folder in (I invariably do). We're now going to do a number of things that are going to transform our structured waste of time into a level;

Mission Objectives

Open up your map and mission file. We're going to add objectives! At the bottom of the mission file is the PrimaryObjectives_StartDefinition section, with NeverTrue in. Which isn't very good. Now, we can be cunning about this - Do we want the player to HAVE to capture the research? If we don't, it'll be auto added by the game as a secondary objective for us, so we can just uh, forget that one for now... anyway, I want the player to activate that red trunk port and the safe area to win, so, I use these lines:

BuildingOnline:ubermcsuxland,1 ubersux_objective ubersux_objective.txt
BuildingOnline:ubermcsuxland,3 ubersux_objective2 ubersux_objective2.txt

Here I've referenced strings and files which don't even exist! But, I've used a standard format which I'm going to remember and won't have to come back here to look up. How did I know which building IDs were the right ones (the bit after the comma)? I had the map file open to look at them, and I set the team of the friendly trunk port to 2, so I could tell it apart from the unfriendly one.

Script Triggers

That done, look back at your mission file in the buildings section, you should see your script trigger! If you don't, you didn't make it dynamic, and it'll be in the map file. Wherever it is, go to the end of the line, to where it says NewScript. I'm going to replace this with, you guessed it, ubersux_intro.txt (you NEED the txt, if your script has a .txt extention which it probably will...) Anyway, we're done here, save but dont close the mission file.

Now we arrange for an outro, in game.txt. Open this beasty up (it's in your root mod folder) and find the Events_StartDefinition section. This bit works just like your objectives bit, so, new line in the section, 'Event ' copy the condition part of the objectives in after each other, so it looks like this:

Event BuildingOnline:ubermcsuxland,1 BuildingOnline:ubermcsuxland,3

Then create another new line, and put something like "Action RunScript ubersux_complete.txt" and then another new line with End (this is pretty important, so don't forget)

You can save and close game.txt now, and unless you don't want to be lazy, the mission.txt file too. But let's be slightly less than lazy and keep the mission file open!