A lot of people were having the same problems as me, as I read thru the posts (most people just spam questions that have already been answered without reading, which makes it harder to find what you need). Here is a basic, and I mean basic walk through to get you STARTED. I'm not going full, because once you know the basics, you should be able to figure the rest out.
EDIT: I did a new start today and edited this. Then went step by step. More thorough and less confusing. My last walk through was not as informative.
1. You start out on your ship. Move with ASWD, aim with holding right mouse clicker and fire with left mouse click. Two fire modes toggles with 1 or 2.
2. On the bottom of the screen there is a journal. Click that, it will give you your tasks. As you can see, you need to build three
Teleport Cells. Build 3 wherever you like. You can move stuff any time while in the build menu.
3. After the cells are built, click on the
Navigation Console, click "
Unknown Signal" and then select at the bottom. Click and hold on the teleport ( not the cells you built, the one connected to the Nav Con) and hit
Yes
4. On the ship, the first person you can see is a "Male" officer. Make sure fire mode "2" is selected, aim and shot at him. One hit should kill him (fire mode 1 is more rapid fire low damage). To your right, there is a button, glowing red, it's the
Bridge Manual Lever. Use it to extend the bridge. To your left is a console that does nothing. Click it if you like. There is a locked chest, encrypted chest, one with materials and two empty. The locked chest key is in the "Optional" portion. Loot the rest or wait to come back.
5. Scan the "male" with holding left click, hit "Yes" and then loot the chest behind him.
OPTIONAL: Now walk to the next
console and use it. All of the people can be one shot with fire mode 2. The drone takes 5 or 6 and he will do some damage to you. Try and avoid his fire while hitting him. Once he is down, keep some distance and take out each human in the room. Far enough away, they won't see you and you can take them down with no trouble. After they are cleared, the room to their right has the key to that chest at the beginning, on top of the three crates. The females wearing underwear in there give you those clothing options if scanned and captured. You can come back and do this area as many times as you like, so no rush to get them.
6. Head to the next
console. Open it and clear your way to the bridge where the captain is.
7. Before you can open the bridge there is another drone to fight. Kill it, go to the end of the hall and use the
console to open the bridge door. You can shoot everything from the doorway. The shots go through mostly everything in there. The captain takes two shots. Make sure you scan the captain and at least two other females before you leave. You can explore more and loot or leave by pressing the "
Evacuation" button on the top right.
8. Back at your ship, Build your
Brainwash 3000 and the
Cortex Extractor wherever you like. Grab the captain from the cell by holding left click. Put her in the Brainwash 3000. Crank the Intensity and Frequency sliders all the way to the right. Set the Duration for 3 hours. This should get her to 9. All the lower you need to go. Now switch the the program to Willpower Suppression. This is done by clicking the brain picture right above the sliders and it will give you a drop down. If you aren't getting a drop down, you are clicking the wrong picture. With the Intensity and Frequency sliders still cranked up, set the Duration to 2 hours. You WONT need the full two hours, just hard to tell you a % of where to have the sliders. Just manually stop it at -10. Now transpose her and put her in the Cortex Extractor. Hit start (the star map is already selected.
After the 2 hours, your journal will auto complete. Now what? You didn't get a new entry to follow!?!? Whatever will you do? How about build some cool new Machines. Didn't I scan a male on that ship? What do I do with him? What is this Bio Printer I can build now? Oh it clones males! But what are they used for? Maybe that Sex Machine I can't get to work with that female all alone. But I WANT MORE QUESTS!!! Didn't I get a star map?? Oh, that Navigation Console probably has some new places to explore. Maybe I'll get quests at one of those!!
I'll stop there. It's straight forward after that. I don't want to spoil it completely. Follow the quest info (Once you have a new quest), it will lead you where you need to progress. You are welcome to ask me questions if you are lost.
Helpful tips-
-Cheat menu is in "options" on the bottom right. Click it and it will fill your resources. (Makes the game really easy and not suggested)
-Machine not working for you? You are missing something. For example, lack of training, resources or required people. Like the Sex Machine requires a male (printed in the bio printer) and a female. Then use the sliders (watch your bio mass cost). Milker will require you to train the ladies first (you can figure it out, there are 9 things to build) Play around, it is a game.
-In machines, click the pictures in the menu to change the action. Examples, Sex machine change from BJ to Vag sex (just like you did for the Brainwasher quest).
Like I said, this is a BASIC guild to get the ball rolling. If I missed something, I apologize, I didn't make the game and I took the time to put in the effort, you can put some in as well. Have fun!