I'm late to the party but wow. What an experience. My heart owwwwww. I also loved how these puzzles have hands and I had to refer to the hints a whole lot to even get a starting point on solving some of them. This kind of thing was exactly up my alley once I realized what it was supposed to be.
Since it took me a while to figure out the final in-game puzzle and there aren't any hints to follow like in part 1, I'll put some of my own plus the solution below so uh yeah spoilers use this if you're really stuck.
It'll be obvious once you're at the final puzzle. It unlocks after you finish reading the audio logs and the computer glitches out.
Hint 1: There's nothing else to interact with on the file screen so the login screen is the only other place to look. That tab contains a jumble of letters and a note labeled "one time pad" with some asterisks underneath it. What does that mean?
Hint 2: Google says that a "one time pad" is also known as a Vernam cipher or more specifically, a Vigenere cipher since we're deaing with pure text. Such ciphers are impossible to decrypt without a key. In that case, where might the key be hidden?
Hint 3: The lines of asterisks seems like a good place to start given their position as part of the "one time pad" block. Asterisks are used as placeholders so we're probably looking for four different keywords that match the length of the strings of asterisks. That makes for two 5 letter words, an 8 letter word, and a 9 letter word. Let's go back to the file screen to look through the documents again, knowing what we know now.
Hint 4: Agent and Aquarist are highlighted in yellow but there aren't any other highlighted words in any of the documents. Think about what they have in common. Are there any other words that might fit in? Perhaps even those outside of the documents?
Hint 5: Agent and Aquarist are designations for different Ames. We can see a third Ame on the bottom corner of the file display: Archivist. The fourth and final Ame is referenced when logging in and when translating the morse code on the login page: Admin. The decryption key can now be constructed, keeping in mind the yellow asterisks.
Hint 6: It's time to decrypt the gibberish. Use this ciphertext alongside your new decryption key to find the password (It's recommended to use a dedicated Vigenere cipher solver you can find online). If your password doesn't work, double check your key. Remember that Agent and Admin are both five letters long!
Step by Step Solution:
Read the documents and audio logs.
Exit out to the login screen.
Note down the ciphertext and lengths of keywords.
Return to document screen and record the designations for the four different Ames: Admin, Archivist, Agent, Aquarist
Use the letters indicated by the corresponding yellow asterisks to create the decryption key. You should get either ADMINARCHIAGEAQU or AGENTARCHIADMAQU depending on which 5 letter word you put first.
Attempt to decrypt the ciphertext with both keys (google vigenere cipher solver). This will reveal ADMINARCHIAGEAQU as the correct key, returning the password IHAVETODIEFORHER.
Input IHAVETODIEFORHER in the login screen to solve.