Welcome to Genesis Alpha One Rank 3 Captain Training.
At the end of Rank 2 Captain Training, you can handle your own infestation. You can handle a SMALL Genesis. You are almost ready to handle a rogue captain attack, perhaps go on the attack yourself. Your ship is defensible. You're probably already at max robots (8, probably 6 movers and 2 shooters). You have shields that will survive long enough for you to jump away.
Now the plans are:
* Go to maximum reactors so you can build the ship to the maximum.
* Make sure we have enough air and quarters to go to maximum crew (and defenses)
* You have maximum shields (with crew) so you can survive (for a little while) in red sectors
* You have ship assault module (so you can attack rogue captains, not just sit there and wait for them to attack)
* You can handle even the largest genesis planets
As for how, you don't really need me to tell you how to do things by now, right? Thought a couple tips bears repeating...
* Keep harvesting and refining minerals so you can make cables and centrifuge so you can gain XP for the crew AND reinforce bits of your ship.
* Keep rotating your crew so everybody is at least a lieutenant, if not a commander, and give every lieutenant and above a better weapon than the default laser pistol.
* Keep looking for gunpowder and sulfur so you can build more turrets.
* Assign your combat robots (if you're lucky to find one) to patrol long routes through danger zones (so they "stir up" infestations so the turrets can shoot them) else you have to go clear them yourself.
As you gain more materials, start relocating modules and add reactors, ship assault, shields, greenhouse, quarters, recreation (cantina and bars), as well as turrets and such to defend them, and clone additional crew as needed until you get the ship maxed out (40 crew, 7 or 8 reactors, max shields, etc.)
Ship Assault (and Ship Defense)
The ship assault module is pretty simple: it's basically the same module as a quarters module, but with a teleporter in the middle and 2 consoles (with an optional third) around. You can use an expansion module to add a third console, as well as add an alien scanner if you wish.
They way ship combat works is your crew will shoot at the enemy ship, and the enemy ship will shoot at your ship, to attempt to bring down the shield. The objective is to beam over boarders to attack your crew, damage/destroy your modules, raid and steal your resources, you get the idea. (Different rogue captains have different objectives, and they are quite obvious. Biomass pirates go after your biotank. Slavers go after your crew, and so on.)
If you are going for two of the achievements, killing fremen or mechanics in defense of your own ship, you may want to unbuild the shields and just wait for them to board you. I am assuming you want to beat the enemy ship and board them instead.
To prepare for combat, you will want to assign one person per shield, which gives it additional power, and over several shields this can be quite substantial.
You will also need at least one expansion module installed in the ship assault to add a 3rd console. Once you got that, assign three people to the ship assault module. Rank and specie doesn't matter THAT much, in my experience. But you can optimize by using Arachnids (better engineers) and the smarter races if you need to eek out every last bit of advantage. For optimum result, join them in the assault module, after you get into range (either you go to them and they come to you) of a rogue captain.
Any way, if you have three crew working the consoles you should win the combat phase, though if you want to be absolutely sure take over one of the consoles and keep processing away. Every full cycle is one salvo, and sooner you beat down the other guy's shields, the less pounding you will take. You, as the captain, are faster than any of the crew, and probably faster than all three combined.
Once the "shooting" is done, your crew will continue processing in order to "scan" the other ship (similar to when you come up to a space derelict/wreck) and locate stuff you can go for (biomass, cargo, blueprints). The captain has no "markings". Though when you kill him he has a blueprint you can pick up. Once all scanning's done, prepare yourself to beam over. I personally prefer to keep a turret in hand.
When ready, step into the beam.
You may be shot at immediately by turrets. Run away, drop the turret, and look for cover. Clear your surroundings. Enemies will look for a path toward you, set up accordingly. Your scanner should alert you to enemies, but that's a 2D scan, whereas your environment is 3D. You can enter 3D view by engaging the "build" view as if you're building something (but you can't on the enemy ship, but it will show you the enemies and damaged modules and more).
Slowly clear section by section toward your objectives. You *can* use enemy ammo and turrets if you can find them in those ammo lockers. Biomass are obviously in biotank modules, and cargo would be in those single cargo modules. Captain can be anywhere, so keep exploring and look for him. If there are other blueprints, they can be anywhere, so just keep using your scanner, but use the 3D view to find it. It could be in the underfloor section too.
Once you've cleared the ship completely (taken all the cargo and blueprints, including the one on the captain), or you decided it's too dangerous to stick around, engage the PDA and return to your ship. You can heal and come back. If you die, you can take over the next captain and beam over again.
Keep in mind you have to clear the ship completely to make it say "cleared" on the sector map. That means you have to have room in your storage or deposit (for cargo) and biotank (for biomass) to drain the other ship.
If you have no problem handling rogue captains, you should have no problem handling Genesis.
SPOILER AHEAD
Going for Genesis
To go for genesis, you need to have the right type of crew (breathing the right air), the right number (enough of them), and the right level (each specie can be tier 1, 2, or 3). If the planet wants tier 2, you can't fulfill it with tier 1 crew. Once you choose that planet, join the crew on the planet.
You need to find the alien queen, and kill it, in the subterrean caves. Then come back to the surface and report to Earth that you've done so.
So what's the catch? Once you made it underground, some medium bug will keep coming at you continually, but one at a time, unless you "wake up" a nest. Every once in a while, your path will be blocked by a barrier, but the bugs can come through. Use a turret to keep the bugs occupied while you use your harvest beam to break the barrier. Keep going, until you find a downward slope to a cave exit.
The queen is beyond that. How far... I have no idea.
I recommend you to put up a barrier to block the cave entrance before you enter the "plaza". Your bullets can penetrate the barrier, they can't push through, not even the queen.
You may want to drop a barrier every once in a while, rotate through your inventory.
Keep advancing, killing the single bugs, until you see the queen, who will charge you. Retreat behind a barrier.
Look for the glowing "egg sacks" on her back, shoot them to pop them. When you pop all of them, the alien queen dies, and you win (but you still need to go back to the surface, and trigger the transmission).
Now, go forth and claim Alpha One for humanity!
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