Repo: The Genetic Opera – Legal Assassin lyrics

While, of course, most, if not all, of the Repo! Songs are literal (they have to be since they're the dialogue of the movie), they still have their layers of symbolism, and "Legal Assassin" is no different.
Throughout the song, you hear a whisper of "Assassin, Murder, Monster" in the background. This is suppose to be Marni's voice whispering in Nathan's head, reminding him of his sins as a Repo Man.
In Nathan's first stanza, he wonders to himself "Where did our daughter go?" Meaning, he's asking how it was possible how much Shilo had changed. "It's me she must escape," saying that, even though he keeps her locked up t prevent the evils of the world coming upon her, it's actually him she needs to get away from, since he is the assasin, murderer, and monster. "My burdens I can't erase," the job of being a Repo Man. "The mother I might have saved," obviously being Marni.
The entire second stanza basically says that she should not fear the outside world, but the Repo Man she is locked up with.
In the third stanza, Nathan says that, despite what he has done, he did not do it on purpose, only with "the best intentions." He needs Shilo to believe he's invulnerable, so he cannot show his weaknesses without Marni being there, and how he's "only living out a lie" as just being a doctor.
The last stanza shows Nathan slowly slipping into his Repo Man personality, going from self-ridicule to praise.