When the foster mother and chief of staff of Martha's, Naomi, is brutally murdered, her adopted daughter, Maddie stays with Martha and Clark. The girl becomes close to Clark and speaks for the first time in years. But when she discloses her power to shatter glass, she becomes the prime suspect for the death of Naomi and her biological mother after Lois voices her suspicions to it. While Clark investigates the origin of Maddie, her powerful father, who also has the same ability, breaks out of prison and abducts her. Meanwhile, Chloe witnesses Lex and Lana too close to each other, and later she accuses Lex of taking advantage of the vulnerable Lana.

Jonathan Kent appears to Clark on his birthday and instructs him that he needs to kill Lionel Luthor because Lionel knows his secret. Meanwhile, Lionel comes clean to Martha about his knowledge of Clark's secret since his possession by Jor-El, and some of his scribblings from his now-telepathic link to Jor-El are revealed to announce that the "Vessel of Zod" is coming. Meanwhile, Lex has another meeting with Milton Fine who tells Lex that he is trying to make a vaccine to protect mankind against an alien virus. When Lana expresses suspicion that Fine is not who he appears to be, Fine reveals his real identity and that "Jonathan Kent" is just another copy of Fine (The Brainiac) sowing seeds of anxiety in Clark.