May, 1986: Clark Kent (Superman) arrives at Lois Lane's apartment, only to discover that she's been kidnapped by the Puzzler, a criminal Superman hasn't seen in many years. The Puzzler leaves a clue to her location, but after he can't figure it out on his own, Superman seeks Batman's help only to learn he's away. Superman then seeks the Riddler's help and is allowed to take him from the prison as long as he returns him in 48 hours. With the Riddler's help, Superman discovers that the Puzzler's clue refers to an Egyptian exhibition at the Metropolis Museum of Natural History. [“DC Comics Presents: Superman and the Riddler: A Puzzle a Day Keeps Superman at Bay, Chapter 1: Kidnapped”]
At the Metropolis Museum of Natural History, Superman and the Riddler find the next clue, a firehouse-turned-restaurant called the Firehouse. Along the way, they dodge various booby-traps left by the Puzzler. [“DC Comics Presents: Superman and the Riddler: A Puzzle a Day Keeps Superman at Bay, Chapter 2: Uncommon Toot”]
The Riddler speculates that the Puzzler is holding Lois Lane to discover Superman's secret identity. Superman and the Riddler find a clue that leads them to Five Banners Over Metropolis theme park, where the Riddler is separated for a few moments while Superman is caught in a kryptonite trap. The Riddler is revealed to be working with the Puzzler, who has been corresponding with him for years, as part of a revenge scheme for the Riddler, who knows Superman is Batman's best friend. Superman then reveals that he has been working with Batman and was prepared for the kryptonite trap, and he captures the bickering criminals and frees Lois Lane. [“DC Comics Presents: Superman and the Riddler: A Puzzle a Day Keeps Superman at Bay, Chapter 3: Wolf in Sheep's Clothing”]