Control

There are 12 side missions to choose from. Three of them lead to achievements of their own, which are all major boss fights in the game, so you'll probably want to attack those three separately. The easiest method is to simply go through the "What a Mess" sequence of missions, all starting in the Janitor's Office. The 12 side missions are:

1 - A Merry Chase. Unlocked during "Directorial Override". Go to the Break Room (down the hall from the Janitor's Office), and the floor will collapse, dropping you into the Astral Plane. Ends with cleansing the Merry-Go-Round Object of Power.
2 - What a Mess: Burn the Trash. Unlocked during "Directorial Override". Go to the Furnace Room and dispose of the hazardous waste barrels. This is pretty easy EXCEPT it's also pretty easy to lose a barrel in accidental explosions while whipping them around the room. You'll have to restart the mission to get any lost barrels back.
3 - What a Mess: Clear the Clog. Visit the mission board in the Janitor's Office. You'll have to clear out the "clog" in the Pump Room (Maintenance). This area is located next to the NSC Coolant Pumps.
4 - What a Mess: Talk to the Plants. Visit the mission board in the Janitor's Office. Just visit all the planters in Research / Central Research.
5 - What a Mess: Clear the Mold. Visit the mission board in the Janitor's Office. These are located in Containment / Medical Wing.
6 - What a Mess: Even More Mold. Visit the mission board in the Janitor's Office. These are located in Maintenance / NSC Coolant Pumps.
7 - What a Mess: Take a Break. Visit the mission board in the Janitor's Office. Not sure why this is a mission, but enjoy the Janitor's Office.
8 - Mr. Tommasi. Talk to Emily Pope. This is a major mission with an achievement of its own (Head of Communications), which is arguably the most difficult achievement in the game.
9 - A Matter of Time. Find the man calling for help in the Logistics area of the Containment sector.
10 - The Enemy Within. Starts after completing A Matter of Time. This is a major mission with an achievement of its own (Living Archetypes).
11 - Self-Reflection. Find the note near Logistics and Security. Go to the Security area, head upstairs, and go through the doors to the Prime Candidate Program. Head down the stairs, take a left into the little security office, and the note is on a cabinet with stacks of folders on it. Another major mission leading to an achievement (Altered Manifestations May Occur).
12 - Old Friends. Talk to Arish in Central Executive.