I just finished the "power rail" and I am confused af

I currently playing half life 1 and I try to pay attention to the dialogues. In the start of the chapter a guard tells freeman that a science team need him to launch a missile to get rip of the aliens. Will they send a god damn nuke? Also the gameplay was extremely weird since you could skip most of the areas without you even realising. Like the troops in the launch silo. What even was there purpose?