A Secret Affair revolves on the lives of happy couple Rafi Delgado (Anne Curtis) and Anton (Derek Ramsay). On the eve of their wedding, Rafi backs out and seeks solitude in the US. Hurt and confused, Anton starts a physical relationship with Sam Montinola (Andi Eigenmann), one of Rafi's friends. Sam's obsession with Anton becomes a problem when Rafi returns and decides she wants to work things out with Anton.