There are obviously supposed to be missions in the game, although I don't know how much you have thought about what they should be, so I'll post some of my thoughts here. BTW is the design you're working to on these forums anywhere? It might save me repeating stuff you have already thought of :)
The beginning and the ending of the game suggest two obvious new missions...
1. Find the "master shutdown" automated colony defense system and disable it, so that a rescue ship can land. The top of the military tower seems like the logical place to find this.
2. Find the communications array controls and send a distress signal. The top of the engineering tower seems like the right place for this.
Then there are the 2 missions that are already implied in the game...
3. Kill the queen
4. Escape the towers
So that gives 4 "critical" missions. As you can see, having the first two in the game would probably mean changing the ending.
If you allow the player to exit the towers without completing all of the critical missions then you'd need multiple endings depending on which ones they didn't do. For example, if they killed the queen and escaped but didn't send a distress signal, they would get the current game ending.
Here are some more ideas for optional missions:
-Retrieve the colony surveillance system logs. These are at the top of the Security tower. This mission is given to you at the start.
-Find the colony superintendent's records. These are found at the top of the Civilian tower. This mission is given to you at the start.
-Find the research report on the alien species' physiology, created by the colonists before the colony was overrun. This is at the top of the Medical tower. You don't get given this mission until you find the colony superintendent's records.
-Kill the juvenile queens. There are 3 juvenile queens in various locations around the towers who are waiting to leave and found their own colonies. You only get given this mission once you find both the surveillance logs and the research report.
-Destroy the hatcheries. In various places around the towers there are groups of rooms that have eggs in them. The eggs are in clusters, and if one egg is attacked then the others in the cluster will spawn juveniles a few turns afterwards. As well as counting towards completing this mission, destroying (or hatching) eggs causes a reduction in the danger level. To destroy a hatchery you have to destroy or hatch at least 75% of the eggs in a hatchery area, and you get experience for each hatchery destroyed. The mission is completed and bonus experience given if you get them all. You only get given the mission once you have the surveillance logs and the research report.
-Find survivors and get them to safety. Survivors would be found mainly in the Civilian tower, in rooms without aliens. You get given this mission when you get the surveillance logs, or when you find a survivor. This mission would be most easily done by simply having survivors being "rescued" when you find them, and disappearing. If you're feeling ambitious though you could make them independent entities who follow the player around and need to be taken to the exit of Civilian level 1... and if you're even more ambitious than that then you could make them able to arm themselves and shoot at the aliens! If you're going to do either of these things then you should let the player tell them when to follow and when to wait where they are by activating them the same way as doors. If you're going to let them arm themselves then you need to somehow make sure that they don't pick up weapons that the player wants.
-The Heist! You remember the Heist, right? :) This quest is a tribute to Tower Assault and would take place on the top floor of the Storage tower. You would be given the mission when you enter the floor. It requires you to find and destroy several "locks". Once you get them all, a door appears to a secret vault room. The vault contains loads of money, which you can't spend, but that's OK because going in there completes the mission and gets you loads of experience that you can spend. The Heist should be done under a time limit of some kind - at least radiation, preferably a proper "countdown to destruction".