The film features a powerful and protective bond between Simone and Cathy, which serves as a central motivator for Simone's actions. This relationship, interpreted as having queer undertones, is presented without explicit judgment or celebration. The narrative integrates this deep connection as a complex and understated element, neither uplifting nor denigrating queer identity.

Mona Lisa features a transsexual character, Cathy, whose identity is central to her vulnerability within the narrative. The film portrays her exploitation by a criminal figure as a tragic consequence of her circumstances, not her identity. The protagonist, George, evolves from initial discomfort to a protective stance, affirming Cathy's worth and right to safety. The story critiques external forces of exploitation rather than her identity.

The narrative focuses on a father's attempts to reconnect with his estranged daughter, presenting a fractured family unit without explicitly endorsing or critiquing traditional or progressive family norms.