Captain Rank

[lackofwords]

For stupid people like me.
The flagged mission is in the squadron mission section NOT command mission section.

Yes, I also got confused due to the vague wording, AGAIN. This happened the first time when they did the flagged missions... which felt like years ago.
I thought it was implying 'do 5 command missions to unlock another flagged command mission.'
Would help if they've appended it to be "a special squadron flagged mission" instead.

By successfully completing command missions at five different locations, you have gained access to a special “flagged mission.”
Due to the exceedingly high difficulty of this mission, however, it is advised that you first improve your squadron members' individual attributes as much as possible before attempting a deployment.