Warning! SPOILERS for The Batman.
Here's the Riddler's plan and all hidden clues in The Batman explained. The Riddler, or Edward Nashton, was an orphan who grew up in a Gotham orphanage, which was formerly Wayne Manor (a nod to The Dark Knight Rises, which also turned Wayne Manor into an orphanage), initially to be funded in part with mayor-elect Thomas Wayne's Renewal Fund. However, the fund was taken over by corrupt politicians and police after Thomas Wayne was murdered, and it was used as a slush fund, robbing the orphanage of its funding, which in turn caused The Riddler to be raised in harsher conditions. He later talks of being housed in a room with 30 other kids, being nibbled on by rats at night, and babies dying of the cold temperatures. He compares himself to Bruce Wayne, who also became an orphan when his father was killed. However, Bruce, unlike The Riddler, was raised in Wayne Tower with all the privileges of a cushy life, instead of a dilapidated orphanage.
Angry about his circumstances, The Riddler grows up to get involved in forensics and accounting, eventually discovering the truth behind what happened to the Renewal Fund and how the corrupt elite had used and abused it for their own greedy means. This realization begets Riddler's intricate plan of clues, riddles, death, and destruction in motion, building a list of targets that include The Mayor, The District Attorney, A GCPD Cop, Carmine Falcone, and Bruce Wayne, all of whom he blames for his childhood trauma, as well as for the perpetual corruption in Gotham City. Seeing Batman emerge in the previous two years serves as the catalyst to The Riddler pursuing his ultimate goals, as he sees him as an ally fighting in the same crusade to bring justice to the corrupt. Ultimately, he wants all of them killed and exposed, with his final act set to murder the newly-elected mayor, then flood the city with strategically placed bombs along the Gotham sea wall.
The attempted murder of the newly-elected mayor, Bella Reál (Jayme Lawson), is the most ambitious of The Riddler's plans, as it involves the use of copycat Riddlers, all of whom are incels that follow him on social media and take up the mission to dress as him and help kill the mayor-elect and anyone else who gets in their way. This all takes place at Gotham Square Garden, where The Riddler's incels assemble in the rafters. It's revealed at The Riddler's hideout that he had been communicating with followers via a 4Chan-style message board, telling them exactly how to prepare while giving them clues and guidance on how to execute his master plan.
No More Lies - The Riddler's Notes And Their Nod To Batman's Rogue's Gallery
Each of The Riddler's clues are left in an envelope, addressed to "The Batman." Inside each envelope is a greeting-card with a cartoonish image, including nods to Batman rogues, such as Court of Owls, Hugo Strange, The Ventriloquist, and Poison Ivy. The first is left at The Mayor's crime scene, which includes a cypher that both Batman and Alfred solve, prompting Batman and Gordon to look in The Mayor's garage, where they find a pair of bloody shears stuck in a car's tire. The two open the car and discover The Mayor's actual thumb connected to a thumb drive, which, when plugged into Gordon's computer, sends out photos of The Mayor with Catwoman's missing friend to every major news source, the first step in exposing the corruption from within.
A Dirty Cop, A Corrupt District Attorney, and El Rata Alada
Additional clues include the rat trap that kills Commissioner Pete Savage, with more cypher codes written inside of it, leading Batman and Gordon to the term "el rata alada" which they surmise is related to a rat with wings in Spanish. The card left with the rat trap also mentions "bringing the rat into the light", which comes into play later. The next clue comes from Batman's confrontation with District Attorney Gil Colson (Peter Sarsgaard) who is captured by The Riddler, a bomb strapped to his neck, and phone taped to his hand. Colson is sent crashing into The Mayor's funeral where Batman also finds another note taped to Colson's chest. The note tells him to answer the phone taped to Colson's hand, which connects to Riddler, who then says that Colson must answer three riddles to save his life. Colson refuses to answer the third riddle, as it would expose el rata alada, prompting the bomb to go off, presumably killing Colson and knocking Batman out.
Where It All Began - Wayne Manor becomes an orphanage
After a confrontation with The Penguin, both Batman and Gordon solve el rata alada (it's a website, where they converse with The Riddler) and are led to the Wayne Manor Orphanage, where they find the words "Where it all began" painted at the entrance. Once inside they enter a room that has a video playing of Thomas Wayne's mayoral campaign (the same Riddler clue video in the online viral video), which talks about the Renewal Fund and even flashes the words "Hush!" over the video. Painted on the walls is "Renewal is a lie," as well as something about The Sins of The Father. This clue prompts Batman to rush to Wayne Tower, fearing that Alfred may be the next target. As he races to get there, Alfred receives a note from The Riddler, addressed to Bruce Wayne (with another note for the Batman, written on fire retardant material), which turns out to be a bomb that nearly kills him. Wayne is able to recover the note, which has the clue, "See you in hell" - although he doesn't know what it means at the time.
Bring Him Into The Light - The Riddler targets Carmine Falcone
After spray painting the clues on the floor and attempting to crack the riddle, Batman eventually is led back to Falcone's underground club, 44 Below, after discovering he murdered Catwoman's friend. After a struggle between Falcone, Catwoman, and Batman, the mobster is eventually apprehended by Batman and led outside to awaiting police officers out front, standing under a street light. At this point, Falcone is shot and killed by a sniper, which turns out to be The Riddler, as Batman had done just what a prior Riddler clue had suggested: "bring him into the light." Riddler was firing from his hideout, which happened to be across the way from Falcone's club. Riddler is captured shortly after in a coffee shop and later Batman is summoned to meet with him at Arkham Asylum, where The Riddler reveals everything but his final plan, telling Batman that he viewed him as an ally and lamenting the fact that he wasn't able to kill Bruce Wayne, as the bomb hit Alfred instead. The Riddler assumed that he would be caught and sent to Arkham, as well as Batman, which prompted the note that reads, "See You In Hell," with "Hell" being Arkham. When Riddler figures out that Batman is not an ally, he taunts him with his final plan, but he gives Batman no clue as to what that might be.
A Real Change - Riddler's Hideout reveals his ultimate plan
Inside The Riddler's hideout is all manner of notes, clippings, ledgers, and paraphernalia from his crimes, including cutouts of Bruce Wayne and his other targets. The words "If only I knew then...what I know now..." are written on one of them. Inside a cage with a bat inside is the last Riddler clue left to Batman, containing a note titlted "My Confession." Batman returns to the hideout after confronting Riddler at Arkham to figure out his final plans and learning that the murder weapon from The Mayor's murder is actually a carpet scraper, called a "tucker". He uses it to scrape back the carpet in Riddler's hideout, revealing a literal "floor plan" for his goal of flooding Gotham, which reads "A Real Change." which relates to the Mayor-elect, Bella Reál. This prompts Batman to rush to Gotham Square Garden where the final confrontation takes place, just as the city is flooded, the mayor-elect Reál is shot, and the army of Riddler incels are taken down, leaving Batman to rescue the survivors and discovering his true purpose as The Batman.
