After Batman delivered Poison Ivy to the GCPD Lockup, Aaron Cash informed Batman that Riddler was seen sneaking around on a nearly trainyard. If Batman chose to follow this lead, he would investigate the location and find a secret elevator large enough to fit the Batmobile. During his way down, Riddler projected himself to the walls of the shaft. Finally reaching the bottom, Riddler challenged Batman to race three laps on a track he designed. Batman successfully completed every lap, and depending on when the mission was attempted, either:
- Returned to ground level, while Riddler sarcastically claimed that he had been defeated once again or
- Helped Catwoman to identify the correct key form several lookalikes.
However, Riddler kept his real plan a secret until later on the storyline.
After Batman hacked the Mercy bridge controls to bring Batmobile to the island, Riddler finally revealed his master plan; He had captured Catwoman and placed an explosive collar on her neck, and asked Batman to come see her in the abandoned orphanage in Miagani Island. Batman complied, and found out that the collar required 9 keys to unlock. Riddler then introduced his new assistants, which Batman and Catwoman proceeded to demolish. If Batman had already completed the first challenge, he was sent to a challenge beneath Chinatown.
The challenge Nigma had prepared required Batman to navigate the Batmobile to a ledge above the starting point to charge the equipment required to help Catwoman. Before leaving, Batman helped Catwoman locate the right key. If the first challenge was beaten before meeting Nigma, he would lower the digit on her collar with two numbers, as a reward for Batman's earlier success. (And to prevent the mission from being unbeatable). Nigma summoned Batman to the orphanage, and made Batman and Catwoman to memorize and tell each other a sequence of numbers to pass the challenge. Riddler rewarded them with more robots, and later, another key.
Riddler then told Batman about the next challenge, located under the Elliot Memorial Hospital. Underground waited another race challenge, titled "Crushonator", with similar rules. To prevent Batman from winning, Nigma had installed pistons on the ceiling of the track, which could crush the Batmobile if Batman was not careful. Riddler referred the amount of pressure the pistons created as "deadbats of pressure". After completing the challenge, Batman again helped Catwoman finding a key.
The Riddler stopped his battle with Batman and Catwoman and ordered Batman to solve all 243 of his riddles in Gotham City. Soon after they left the building and a brief chat, Catwoman left the area.
Batman solved all of Nigma's riddles, and returned to the orphanage. As he promised, Riddler "allowed" Batman to fight him. During the battle, he turned most of the robots red, thus making Batman unable to even touch them while Riddler shot lasers at Batman. Much to Nigma's annoyance, Catwoman, who had been hiding in the orphanage, jumped in to help Batman. Together, they defeated Nigma.
Outside the orphanage, Batman revealed Selina that they would not see each other again. After a brief speech, the two kissed for the final time, and Batman drove Riddler to the GCPD lockup.
- If Batman activated the blockade before the Riddler stopped listing the rules, he would be confused and nervously claimed that it was in fact, the very first riddle.
- Players completing the side-mission for the first time should equip the default Batmobile model for the final part even though it's not required for anything, as using any special models can skip over the cutscene afterwards. This makes it possible to accidentally miss Batman's speech and the closure of his and Catwoman's relationship.
- Due to length of this side quest and Batman's speech to Catwoman in the end of Gotham needing a new legend worse than him, it is believed that canonically this is the last mission Batman finishes before the Knightfall Protocol.
- The first time the game is beaten, it's not necessary to capture Riddler; most players get annoyed and give up on trying to solve his challenges due to how obscure some are.
- When only 10 "riddles" are left, Riddler radios Batman to try intimidating him into not coming back to finish the fight. However, it's obvious by his voice that he is scared at the idea himself.
- After half the challenges are completed, Riddler snaps at Batman every time he completes one; he claims that his challenges weren't finished and to return the trophy, or sneer that he rewards intelligence and not initiative.