I used to write guides and howtos for my guild and since the server is down for maintenance I figured I can write a quick one.
Guide to Starbase Incursion
Enemies of the Federation has snuck on board the starbase and are trying to sabotage its operations. It is up to you to deal with them.
The primary objective of Starbase Incursion is simply to stop as many saboteurs as you can. The most important thing to remember is that amount of fleet marks you ear is directly tied to the number of saboteurs you manage to stop. So kill as many saboteurs as you can! The best group I have ever been in managed to kill 45 saboteurs and we earned 44 fleet marks. I have heard of groups earning as much as 48 fleet marks.
Saboteurs are usually hacking into a console and can be easily identified by the blue progress bar hovering above their heads. The progress bar is an indication of their progress in disabling your starbase and when they have successfully completed their job, they will beam out.
To be successful in Starbase Incursion, each member of the team must be able to work independently but also work as a cohesive team. Most of the time, each member of the team must work alone in achieving the objectives. It is vital that all team members must have the ability to take down saboteurs by themselves and still be able to stay alive despite overwhelming odds. So make sure you have a good mix of offensive as well as defensive abilities, and remember to bring a couple of hypos to keep yourself healed.
The ground map is a dark maze-like warehouse that is divided into four quadrants with an open area in the middle of the map. Players have taken to labeling the quadrants "Top Left", "Top Right", "Bottom Left" and "Bottom Right" with "Top" referring to the two quadrants farthest away from the team's spawn room and "Bottom" referring to the nearest two quadrants.
Other than the final fight which takes place in the central area, most of the action takes place within these four quadrants. Learn the layout of the four quadrants. Be familiar with where saboteurs usually beam in. I would suggest that after completing the mission, spend some time walking around the maze and try to remember the layout of the four quadrants.
Three Phases of Starbase Incursion
There are three phases to Starbase Incursion. The objectives in each phase is the same: Kill Saboteurs. The only difference is the number of saboteurs in each phase. There are at least 45 saboteurs in phase 1. Phase 2 only has 4 saboteurs and phase 3 only has a single saboteur - the boss himself.
I am not 100% certain about this but the duration of each phase seems to be tied to the number of saboteurs killed in the previous phase. So the more saboteurs you kill, the more time you have to complete the objectives in each phase.
In Phase 1, saboteurs will randomly transport in at random locations throughout the map. Your task in this phase is to roam around and kill as many saboteurs as you can.
In my experience, as much as 80% of the fleet marks you can earn will come from this phase. So let me repeat this again, kill as many saboteurs as you can.
Ignore anything that isn't a saboteur. Leave the non-saboteurs to your shard of possibility clones, security escorts, mortars, phaser turrets, combat drones and pets.
There are only four saboteurs in phase 2, one in each quadrant and they are always in the same spot (unless someone attacked them). This time, the resistance is a lot stronger and each quadrant is filled to the brim with enemies. Fighting your way in is often not a viable option as you won't have enough time to blast through everything.
Create a distraction with your pets (security escorts, mortars, turrets, combat drones) and while the guards are busy, run past them and make your way to the saboteur.
Personally, I prefer to use the cloak that comes with the Omega Ground Set earned from STFs. It allows me to simply dash past most of the guards. Granted, a couple of guards will be able to detect you so make sure you have some form of defense to keep you alive while you attack the saboteur.
For Engineers, a Cover Shield behind you works wonders as it blocks off all attacks on you, allowing you to concentrate on killing the saboteur. Science officers can use a mix of Dampening Field and heals to stay alive. As for Tactical Officers, lets just say a strong offense is a good defense.
Team coordination is important in phase 2. Make sure you call out when you have killed a Saboteur so team mates don't waste time trying to find an already dead saboteur.
Phase 3 is pretty simple, there is only one Saboteur - the boss himself. The only catch is he has raised a force-field around him. You have to kill all his guards outside the force field before you can disable the force-field and kill the boss.
Remember I mentioned that the amount of time given to you seems to depend on the number of saboteurs killed in the previous phase? If you killed 0 saboteurs in phase 2, you will have as little as 30 seconds to kill the boss. If you killed all 4 saboteurs, then you have a comfortable 2 minutes 30 seconds to kill the boss.