The following 5 achievements/trophies will all come with story progression, so as long as you finish the game these should be pretty much un-missable. As these contain plot elements, I have left off the descriptions to avoid potential spoilers.
Note that there are some other, missable story-related achievements/trophies. They are listed in the below mission-specific achievement/trophy section.
|Rabbit||Complete the 'Sparta' level.|
|Secret||Complete the 'Korbut' level.|
|Within a Hair of Death||Complete the 'Revolution' level.|
|Big Momma||Complete the 'Undercity' level.|
|Revelation||complete the 'Polis' level.|