To open the locked security doors in control you need to step up the Clearance Levels. Clearance Levels are important to advance in the game anyway but are important to open the security doors as well.
As you progress in the game, you increase your Clearance Level. When you go near the doors, they will be locked and will require levels of Clearance Levels. As you explore the Oldest House you will be finding the Security Cards.
As you acquire these Security Cards, you will be increasing the Clearance Levels along with that.
Clearance Level #1 Card
You will obtain your first Security Card once you reach your second mission. You have to enter the Mail Room but it is locked. You have to look around and you will find a guard on the floor, probably dead.
You are going to find the Card near his body and with this, you reach Clearance Level #1.
Clearance Level #2 Card
You have to continue in the main story here and when you reach your third mission, you are told to go and meet the janitor downstairs.
Go and take the elevator and meet him. He will take you through some objectives before giving you the clearance for level 2.
Clearance Level #3 Card
To acquire the card for this is no trouble at all. At the very end of the third level, in the Executive Area, the Pope will ask you to follow Marshal to the Research Sector.
This whole area requires Clearance Level #3 whose card will be eventually given to you by the Pope. Now you can go and enter the area.
Clearance Level #4 Card
When you solve the puzzle at the end of mission 4, Old Boys’ Club, you are going to speak with someone. She will take you through your next objective and will provide you with Clearance Level #4 Card as it is required to enter it.
Clearance Level #5 Card
In your fifth mission, you will be looking for a Black Rock. Your path is blocked by a locked door that requires Clearance Level 5.
To reach that level, you are going to go to the table near you that plays one of the Doctors videos and pick up a document that is going to give to Clearance Level #5.
Clearance Level #6
This is pretty simple. You are going to finish your sixth level and enter the next scene. You are going to find the last Clearance Level here.
These are all the Clearance Levels and the ways of progressing through these levels. All these missions are completed in the main story and are continued here.