Story related and unmissable. This second mission is significantly longer than the first (around an hour for me but I'm ocd about exploring EVERYTHING in this type of game) and introduces several new gameplay mechanics such as sneaking, distracting enemies, using a Maintenance Jack to open certain doors, etc. Note that you will see several doors that require an Ion Cutter. Don't worry about them as you can't acquire the cutter until later in the game at which point you can backtrack to unlock the doors. This is a super easy level as enemies are virtually nonexistent.
There are also 17 collectables to be found here. If you want a great youtube guide, check out Maka91Productions.