The puzzles here are listed mainly chronologically, in order of intended solving. Some mistakes may be present, but information should be fairly reliable.

Minor spoilers ahead, as this page will tell you what to look for and where. Solutions are not given.

Puzzle 1

This is likely the first place you'll start solving, and the goal can be found in the tablet's logs (click on the button on the left of your screen to access your tablet).

Hint 1

There's notes around the facility, have you read all of them?

Hint 2

There's two types of notes, do the yellow notes stand out in any way?

Hint 3

There are bolded characters, and each note has a roman numeral. Does arranging the bolded characters in order give you anything?

Solution

Use a ROT13 cipher on the text you got from the bolded characters. You should get CLEARANCE T4 LOG. Try this answer as a password, then consider that spaces aren't very common in passwords.

A full (albeit in-character) solution, as well as the full log text can be found at Incident False Start.

Where to find everything needed

The solution is submitted for Incident: "False Start" in the logs. This is indicated by the solution.
The yellow note locations can be found at Yellow Notes, expanding the boxes will reveal the contents of the notes.

Post-solve Hint

There's a ciphertext within the log, haven't you seen something that looks similar before?