How To 

How to Issue the Evacuation Order in Fallout 4

During the mission 'The Nuclear Option', which is the last mission of the game to get the Minuteman ending, you are going to receive the quest to issue the evacuation order. This is an optional mission objective for this, so read on and I'll explain how you will do this.

Step 1)Teleport the rest of the minutemen inside.
You'll do this by accessing a console within the institute that you'll have to load a holotape into with the coordinates for Sturges to lock on to and teleport everyone inside. It's not too far into the institute from where you came in, and the Nuclear Option quest will point you directly to it. Speak with Preston once he is there and he will let you know you need to plant a fusion device on the reactor to blow the place up. He'll also mention that you should evacuate the civilians so as to not perform mass murder. That's where you get this quest object from.

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Battle your way through the synth's until you reach Father.
The quest objectives will be showing you where you need to go here, but there's going to be a lot of synth's between you an your destination. Once you have battled your way through them all you'll find Father. If you have high skills in persuasion you can convince him to give you a shutdown code for the rest of the synths, this isn't necissary for this objective at all, but does make the rest of the quest easier to accomplish if you can talk him into it.

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Step 3)Issue the evacuation command.
Whether you convince him to give you the code or not, access the terminal behind him, no password or hacking is required, and one of the options listed here is to issue the evacuation order. Select that, and your optional objective is complete.

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That's it, the civilians will run for it, and you won't have to deal with them getting caught in the crossfire while you make your way to the reactor to blow this place sky high.