The protocol was followed after the main story's ending as well as completing 7, 12 (New Game Plus) or all 14 of Gotham's Most Wanted Side Missions (excluding The Season of Infamy missions). In the Knightfall Ending, several reporters (Including Vicki Vale) were seen outside Wayne Manor waiting to interview Bruce. However, after he saw that all his most hated enemies knew his identity, Bruce concluded that the protocol must be activated in order to ensure that Gotham City's citizens stayed safe to a relatively stressed Alfred. Moments later, Bruce walked inside the manor when he activated the explosives, which blew up the mansion
and apparently killed himself and Alfred with the blast — however, it was unknown whether they truly died, or that the Knightfall Protocol was about faking their deaths.
If you completed all 14 or 18 of the Most Wanted Side Missions, Commissioner Gordon was seen by the Bat-Signal while narrating a speech about crime and how Batman's sacrifice allowed the people to live relatively normal lives and who would stop crime, seeing as how Batman was dead. In an alleyway, two thugs robbed a family that was similar to how Bruce's family was robbed. One thug told the other thug to take the unconscious man's wallet, when he saw what appeared to be Batman standing on a roof. The other thug told the mysterious bat figure that Batman was dead and how they were not afraid of him anymore. However, something was not normal as the bat figure rose. Seconds later, the figure expanded to a fiery bat creature that released hundreds of bats on the thugs and flew toward them. There were a few speculations on what the ending truly meant because there was really no hard evidence to conclude:
- Batman faked his death: That was what most seemed to think the ending was (Because Batman wouldn't kill Alfred). After the mansion exploded, Bruce Wayne/Batman was presumed dead. Some people thought that before the explosion, Bruce and Alfred may have went down into the Batcave to shelter themselves from the blast. In the 100% Ending, where it showed Batman on the roof in the end, some believed that it may have been Bruce under the cape and cowl. (People already saw the mansion explode, so they may have thought that Bruce was dead and that this was another Batman). Others believed that it was another under the cape and cowl such as Azrael, Jason Todd, or some other member of the Bat Family possibly either Dick Grayson or Tim Drake. Some even believed that the new Batman was either Terry McGinnis or Damian Wayne. It was unlikely though, seeing as Terry wasn't born yet, and there was no real evidence of Damian's existence other than Talia al Ghul's remark in Batman: Arkham City. Even then, Damian would not be old enough. It was also possible that the new Batman was Jim Gordon, as he had, in fact, taken up the mantle in the comics, and he was the one who said that Gotham needed a new savior. (Note: The Batman in the ending resembled the Batman from the hallucination in the main game. That suggested that this Batman may have been using Scarecrow's Fear Toxin.)
- Batman is dead, and Gotham used Fear Gas to control criminals: Some believed that to be a possible meaning to the ending as well. After the explosion, Bruce was dead. There was no Batman on the streets to control criminal activities in Gotham. Some people thought that the city was using the Fear Toxin to control criminals and strike fear into their hearts after Batman's death. (That seemed unlikely as well due to the fact that the Fear Toxin should have affected the innocent bystanders in Gotham as well as the criminals.)
- Bruce Wayne is dead/incognito, another took on the mantle: Another possible meaning to the Knightfall Protocol ending was that Bruce was indeed dead or in hiding, but another Batman took up the mantle. Fans speculated that the new Batman was either Red Hood (Jason Todd), Nightwing, or Azrael. Azrael initially seemed to be a strong candidate, but was actually unlikely: he was previously interested in becoming Batman's successor, but ultimately either gave up on his mission upon discovering he was being manipulated by The Order of St. Dumas, and turned against them — or, more revealing, tried to murder Batman and was arrested by him, which did not alter the ending, and indicated that it's not Azrael.
- Bruce Wayne is or isn't dead, the ending was figurative: Another possible meaning was that, following Bruce either committing suicide or faking his death, the citizens of Gotham were inspired by his sacrifice and fought back against crime, unlike Thomas and Martha Wayne. The family at the end could be a metaphor for Bruce's family, as the mother at the end had the same necklace as Martha Wayne and they were going out of a movie theater. The giant bat was a metaphor for someone coming in to stop the thugs and save the family. The citizens fighting back against crime would allow Tim and Barbara to get married without any issues and would fulfill Batman's mission of not letting another 8-year old boy lose his parents to crime.
- Batman in the ending cutscene is a figment of the thug's mind, and a result of exposure to Crane's new Fear Toxin: It was possible that because only thugs were left in the city, as normal citizens left, that people who committed crimes were the only ones exposed to the Fear Toxin when Scarecrow spread it through the city. As was said throughout the game and experienced by Batman, exposure to the Fear Toxin caused long-term psychological damage. That may manifest itself in criminals in Gotham as Batman appearing whenever they are doing something and fear Batman would arrive. It could be akin to Batman's visions of the Joker, but more terrifying as the criminal's fear of Batman was different from Batman's fear of turning into Joker.
There was no real hard evidence to confirm Bruce's death, because his body was never shown. In the Post-Story Arkham Episodes, several thugs refer to a "ghost" that apparently was stopping crimes around Gotham, hinting that there is a physical entity. Whether or not it's Bruce or someone else is not elaborated on.
- The Knightfall Protocol was very similar to Protocol 11. That was because both were protocols which involved failure to some degree: Knightfall for being the failure to keep Batman's identity a secret, and Protocol 11 for being the failure to stop any party that disabled Protocol 10 and when Hugo Strange lost. Also, both had explosions which may have resulted in death.
- It was currently unknown if Alfred and Bruce died in the explosion at Wayne Manor.
- Commissioner Gordon repeated the line he said in the beginning of the game after Wayne Manor was destroyed and Bruce was "dead": "This is how it happened, this is how the Batman died."
- Throughout the final cutscene, there were multiple billboards that implied that Gordon became Mayor of Gotham City. This is confirmed on the GCPD Lockdown Arkham Episode.
- Tim Drake got married to Barbara Gordon in the 100% Complete Ending.
- The Knightfall Protocol was foreshadowed several times in the game, as several thugs speculated Batman's true identity. Furthermore, after he saved Catwoman from the Riddler, Batman mentioned that he wasn't capable of protecting Gotham anymore, and that a new and more powerful legend was needed and would rise from the ashes of Batman, which implied that Bruce already had a replacement in mind for the Knightfall Protocol. Furthermore, after he caught Penguin with Nightwing, Bruce said that he was proud of Dick and wanted him to promise that he would keep Blüdhaven safe and told him that after tonight, they would never see each other again, which implied that he didn't choose Dick to be his replacement.
- Batman was notorious for faking his death in other media, such as The Dark Knight Rises, where he faked being killed in a nuclear explosion while Bruce Wayne was apparently killed during the riots in Gotham. In the classic comic/movie adaptation, The Dark Knight Returns, he faked a fatal heart attack. Bruce also faked his death in Batman: The Animated Series in the episode: "The Man Who Killed Batman" by faking his death via explosion, and possibly hinted at his true fate.
- The explosion of Wayne Manor was a reference to The Dark Knight Returns, in which Bruce faked a heart attack and Alfred died of a stroke.
- Lex Luthor (possibly) and Calendar Man were both seen in the crowd during the protocol.
- If Bruce indeed died in the explosion, his death shared some similarities with Joker's death: They were both overwhelmed and worn down by something from their past (Titan and Jason Todd/Scarecrow), and were both responsible of their own deaths, with the other one involved. The main difference was that Joker's death was an accident caused by his greed, while Batman's death was caused by Scarecrow exposing his real identity to Gotham and (possibly) the world.
- It was very possible that the "Phantom Bat Figure" in the end was indeed Bruce Wayne due to the fact that when Crane was exposed to his own toxin at Arkham Aslyum, he saw Bruce as a similar Bat figure.
- In the many Gotham City Story DLCS that took place after the fateful last night of Batman, the Knightfall Protocol was mentioned by thugs and the main villains who often said that Batman was "dead" or Two-Face when he mocked Robin and said: "He couldn't protect the city while he (Batman) was alive." That confirmed that almost all the villains and thugs knew that Batman was "gone".