The story opens in some sort of diabolical laboratory where The Joker is holding a very pregnant Lois Lane hostage. The Joker accuses Lois of being "Mrs. Superman" when she informs him that her husband (Clark Kent) will have contacted Superman to come to her rescue. As if right on cue, Superman burst through a window and on to the scene. Joker quickly exposes a concentrated lump of green kryptonite and Superman consequently crumbles to the floor as his powers start to fade. But what's this??? It seems that Joker's been tricked. The so-called Superman bends Joker's hand back, forcing him to drop the kryptonite. A shot is fired at "Superman", and Lex Luthor is holding the smoking gun. The scene ends with Lex basking in his smug assurance as he removes the latex "Superman" mask from the cowled face of Batman.
To shed some light on the previous scene the disembodied narrator brings back to twenty-four hours earlier to the BatCave where Alfred Pennywise and Batman are engaged in a heart to heart about Dick Greyson's future. It seems that Dick has decided to leave the Wayne Manor to pursue an academic career, and this has left Batman wondering how he will proceed without his partner-in-justice. Deep in thought about the situation, Batman is pleasant surprised when Robin shows up on the scene to help his mentor with the case.
The Dynamic Duo show up in Commissioner Tony Gordon's office, the self-same office where his father Jim Gordon once operated out of. Tony directs the duo to the site of a break in at the Gotham Metallurgical Institute. Batman and Robin arrive on the scene to find a small lab (not the same as the one Joker will be holding Lois Lane at in twenty-four hours) in total disarray after a robbery perpetrated by none other than The Joker. Batman discovers after questioning a technician that while nothing of great value has been stolen, that which was stolen explains The Joker's reason behind the robbery.
In the first appearance of any bat-vehicle, The Dynamic Duo is off to Metropolis in the Bat-Jet, and meet up with Superman along the way. Returning to the present we find Superman and Robin standing on a rooftop. Superman dictates the events of the first scene in this episode to Robin, as he is watching them with his X-ray vision. We learn to important details. The first is that The Joker and Lex are have teamed up to do something nasty to Superman, but to kill him. The second is that The Joker is only helping Lex because Lex freed him from a Soviet Gulag. Lex hoped to employ The Joker's extensive knowledge of Gotham to obtain the kryptonite from the Institute.
Finally the confrontation begins. Robin, dressed as Superman offers to accept any mistreatment that Lex would desire to impose upon him, and to not use any of his "super powers" in his defense. Lex accepts the arrangement, but has Lois put behind a lead shield to prevent any "further" damage to her unborn son. Robin indignantly wonders aloud about what harm could have happened, and Lex reminds him of the green kryptonite that was exposed earlier. Just as lex is about to expose the gold kryptonite, which would remove all of Superman's powers forever, two beams of heat vision melt the lead box containing the item. Enter the real Superman. A small scuffle ensues, but in the end Lex manages to get himself and an unconscious Joker into a get-away-rocket, and the heroes escaped just before the building explodes.
In the comfort of an unidentified office, Superman reveals how he managed to protect Batman from a fatal bullet wound earlier. Through a combination of heat vision and super-breath, the bullet was destroyed and the effect of taking a bullet to the chest was mimicked. At the same time, Batman used an ancient Tibetan technique to slow his heart. There is also discussion about the future of the unborn child of Lois and Clark. Superman discovers that the boy, to be named Joel Kent, must have been exposed to gold kryptonite because his atomic structure has been "realigned". Together the couple decided, with encouragement from a suavely dressed Dick Greyson, to keep the nature of Joel heritage from the boy.
Batman and Robin return to the Manor discussing the possible outcome of Joel's life and Batman's hardened view of the world. Meanwhile back at the manor, an unidentified woman approaches Alfred, and both are wearing bee-keeper's outfits. The woman has something important to tell him. While telling this to Alfred, we can see that the woman is holding a partially knitted baby bootie behind her back.