Jimmy thinks his estranged father is an engineer. Instead he's a suave spy with a lethal agenda.
A man from NIA gives Lois a burned computer before he dies and Lois asks Jimmy to retrieve the information from it since many people seem to not want the information go in public.
Meanwhile, Jimmy's father, Jack returns to Metropolis after 4 years. While all this time Jimmy thought his father was an engineer, in reality, Jack is a spy who works for the NIA and is asked to get the burned computer as soon as possible by any means necessary.
Jack aborts the mission when he learns that Jimmy is involved and has to kill him.
When he learns what his boss Trevanian was planning to do and why he wanted the computer, he helps Superman prevent the catastrophe and comes to an understanding with his son. Jimmy has excepted who he is and only wants him to try to be his father.
Clark and Lois were thinking about children and when Clark saw what Jimmy's father had to do - abandon his son - to save the world, he was afraid that this might happened with him and his child as well. Lois tells him that this would never happen because he will be a good father and will put his family first.