Anytime you’re thrust into a mission with Bode or Merrin as companions, make sure to use RB + B to direct them. Turns out it’s incredibly handy, so whenever Bode or Merrin’s diamond-shaped icon fills (it’s on a fairly short cooldown), be sure to call them into action. Ten times each isn’t much, so as long as you remember to do this, it’ll come very quickly.

This is missable, so if you do happen to forget, you’ll have to start a new story save (or New Game+, if you like) and try again.