Star Command is a pretty neat game, but it can get extremely overwhelming and confusing, especially if you don't have simulation experience. Once you get the hang of things though, it becomes not only manageable, but a times, easy.
Here's a few tips to help you get started, Captain!
Your crew members may wear any hat they need to (red - fighting, yellow - fixing, or blue - healing), but relegating them to one job will let them master said job, and gain special abilities. One of the most useful is the yellow ability to increase the repair AOE, which allows them to repair hull breaches without getting in their proximity and getting sucked out into space.
If you're having trouble with the zombie mission, convert every crew member possible into a Redshirt (two for each weapon, four on the bridge), and assemble everyone in the bridge, with their backs to the wall. The zombies will wander in the room and will be eradicated before they can do anything.
In order to generate a dodge token, you need to have at least one Yellowshirt in the dodge room. To generate ammo for your ship's weapons, at least one Redshirt needs to be in the weapon room. Remember that in case you're wondering why your dodge and weapon meters aren't rising.
The engine room and the bridge can accommodate four Yellow and Redshirts each, respectively. Although, you do not need to have any of them stationed there, as those rooms do not do anything outside of enact your upgrades for either room -- leave one person there for the upgrades, but put them somewhere else and let those rooms get destroyed if you're having a tough time as they are not nearly as mission-critical as the weapons systems.
You can actually target enemies in combat by tapping them. Sometimes, choosing to guard an area with your AOE range is more ideal, as you don't want to follow an enemy into a breach or fire, but it is an option.
Don't forget to repair after every fight. You don't want to go into the next skirmish with a burning room or hull breach -- although sometimes, you might -- more on this later.
The laser gun has the hardest mini-game out of all the available ship weapons. You have to press all three dots in sequential order, going from the fastest dot to the slowest. It's not always in the same order and it's very hard to get into the swing of things.
On the flip-side, the machine gun and plasma cannon minigames are super easy to do.
Camp out in the blue healing room if you run into trouble. This is an invaluable strategy for stronger hordes that board your ship. Camp the healing room. You will recover 200% more health (if upgraded), and this will stack with blue healers.
You can pretty much fight off any intruder with this ball of healing -- just try and keep at least one Redshirt in a weapon room so you can actually recharge your weapons. You can also camp a weapon room with a ball of blue and red crew members to ensure that you're always firing back.
Save your dodge tokens for critical hits -- you don't always need to dodge every oncoming attack. If a laser beam is going to smash into a non-critical area, let it hit that area. Save your tokens for attacks on crucial areas, like the middle of your hull (which makes it very hard for units to escape if there's a vacuum sucking them out).
Speaking of getting sucked out, use hull breaches/vacuums to your advantage. If your weapons systems are in a corner and you already have two Redshirts in there manning the guns, a hull breach that protects their area from intruders lets them stay in there and do their thing.
In a few battles, I've actually easily won fights by having enemies constantly get sucked out while I simply stay in my room and trade blows. It's a lazy oversight -- your ship cannot explode -- the enemy must kill your Captain or the Princess. As a result, you can game fights using hull breaches to "guard" rooms.
You can grind tokens by flying around the galaxy map and looking for yellow dot encounters.
Always err on the side of caution when it comes to dialog options. If a situation seems to good to be true, question it. You might just end up uncovering a plot to trick you.
You can save before every fight, in a neutral/safe zone. Keep at least two save files and alternate. You may end up recovering a past file to get out of a jam.
New Game+ is where the game really begins. Once you obtain a bigger ship, it's much harder to manage your rooms. Follow all of the above tips to maintain control of the bigger micro-management task ahead of you. When you obtain grenadiers, you can bomb your own walls to enact advantageous hull breaches.
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