Jacob Keyes is the Lieutenant that is assigned to pilot Dr. Halsey's vessel and protect her at the beginning of the novel. He also accompanies Dr. Halsey onto the school playground to observe and run a test of Number 117, which is John. Keyes's naval personnel record is less than stellar. He is busted down in rank at the beginning of the novel for refusing to testify against his commanding officer.
Her record for keeping a secret and remaining loyal to his commanding officer, even against adversity, is the reason Dr. Halsey chooses him to escort her. Keyes works his way back up in rank over the years. He is the captain of the Iroquois when Halsey chooses him again to pilot the ship, Pillar of Autumn, for a new Spartan mission.