Rae is a freshly dipped pure strain human who experiences feelings of sorrow and loneliness for reasons unclear to him. He knows he is supposed to guard the Master and his operations, and has been led to believe Unity is a force for peace, but being so recently mutated he is still troubled by a vague memory of his previous life.
↑There was at some point a cinematic planned when getting Rae to kill the Master as detailed in PIPBOY.MSG, line 87: (under the section/heading "Movie archive titles"). There is no such cinematic in any of the Fallout data files, however.