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The story details Daredevil's fall to insanity and destitution at the hands of The Kingpin, as well as his subsequent struggle to build a new life for himself. It is considered by many fans to be the definitive Miller-written Daredevil story.
Karen Page, the former secretary of the Nelson & Murdock law offices and girlfriend of Matt Murdock, left the series years earlier to pursue an acting career in Hollywood. However, her plans did not work out, and she became a star of pornographic movies and a heroin addict. Unable to take control of her life, she spirals deeper and deeper into an existence of hunger, need and desperation, until she finally sells Matt Murdock's secret identity for a shot of heroin.
This information eventually reaches the Kingpin, who proceeds to test it. Over the next six months, he uses his vast influence to hound Murdock, causing his accounts to be frozen by the IRS, the bank to foreclose on his house and in general make Murdock's life increasingly unbearable. He even manipulates police lieutenant Nicholas Manolis into testifying that he saw Murdock pay a witness to perjure himself in a case. In the resulting trial, Murdock manages to avoid a jail term, but he is barred from practicing law. The Kingpin skillfully ruins Murdock's life piece by piece, but Murdock cannot see his handiwork – instead, he is convinced that he is simply unlucky and that there is no enemy for him to fight except for his increasingly desperate and violent attempts to investigate this situation.
But the Kingpin overreaches himself. He can't keep himself from delivering one more strike, and he has Murdock's house firebombed - a signature mob act. This tells Murdock that his problems were not random, isolated incidents, but a "masterpiece" of personal destruction - which the Kinpin "signed".
Unfortunately, by now Murdock has become unhinged. He has trouble differentiating between his fantasies and the real world. He is homeless and absolutely destitute, and now believes he has no friends. He even thinks that his former girlfriend Glorianna O'Breen and his best friend and business partner Foggy Nelson are a part of a complex, all-encompassing conspiracy against him.
Meanwhile, Murdock's confidant, Ben Urich, the Daily Bugle reporter, is investigating his friend's plight and finds evidence of the Kingpin's involvement. Unfortunately, the Kingpin learns of this and has Urich's source killed and Urich's hand broken to intimidate him into silence. This cows Urich into keeping quiet and Murdock is left on his own.
Seeing no other course of action in his confused and paranoid state, he decides to attack the Kingpin and force him to return his life. On the way, he brutally assaults three would-be robbers in a subway train and then beats up a police officer who attempts to arrest him and takes the officer's nightstick. In his weakened and confused state, he is allowed to enter the Kingpin's office and quickly beaten by the crime lord. The badly hurt and unconscious Murdock is drenched in whisky, strapped into a taxi cab, whose owner is beaten to death with the billy club Murdock stole from the cop, and finally, the taxi is pushed off a pier into the East River. When the car is eventually found, Murdock's reputation will suffer the final blow. The Kingpin revels in the knowledge that he has completely disgraced, destroyed and murdered the only good man he ever knew.
But when the taxi is finally found, there is no corpse. Instead of drowning, Murdock managed to smash the windshield and, in a supreme show of will, cut the safety belt with one of the fragments and swam to safety.
Badly injured, Murdock stumbles through New York's Hell's Kitchen by sheer will power alone, and, though injured, forces himself to keep walking just to keep from passing out. As he shambles aimlessly across the city, he is stabbed by a thug in an alley and even hit by a car. He eventually ends up being rescued by his mother, who, having not been in Matt's life for decades, has become a nun at a local church. She nurses him back to health. At the same time, Karen Page – now hunted by Kingpin's men as part of Kingpin's orders to kill anyone who possessed knowledge of Murdock's secret identity – arrives in New York with an abusive drug dealer named Paulo Scorcese, intent on finding Murdock. She's unable to locate him, but meets up with Foggy Nelson, who takes her to his home in an effort to protect her from Paulo. Meanwhile, Urich manages to regain his courage and comes forward with his investigation, alerting his paper and the authorities of the situation.
In the meantime, the Kingpin becomes increasingly obsessed with finding Murdock and silencing Urich. He first arranges for the nurse who murdered Urich's source to kill the reporter himself and he also arranges for a violent mental patient to be released from an asylum, dress up as Daredevil and kill both Nelson and Page in an effort to provoke Murdock into resurfacing. However, Murdock intervenes in both plots, defeats the nurse and the patient, takes the latter's costume and proceeds to save Page from both Scorcese and another hitman sent by the Kingpin. The two are reunited and Matt comforts Karen with the fact that he has moved beyond regretting losing his material possessions.
In a major misstep, the Kingpin uses his connections in the military to procure America's super soldier, Nuke, whom he sends to assault Hell's Kitchen. In a climactic battle, dozens of civilians die while Matt responds as Daredevil for the first time since the destruction of his home. Nuke uses heavy weaponry against Daredevil, who is plagued with not only the challenge of fighting an inhumanly formidable opponent, but the awareness through his enhanced senses of the casualties caused every time Nuke's weapons are fired. In the end, Daredevil defeats Nuke and, in an uncharacteristic move to stop the slaughter, uses Nuke's weapon to destroy an assault helicopter that supported Nuke and further threatened civilians, thereby killing the pilot. The Avengers arrive at the scene and take Nuke into custody.
Captain America, however, is not pleased with the situation. Although the authorities claim that Nuke is a terrorist, the Captain is not convinced, especially after a discussion with Murdock, who tells him that the assailant's body was heavily enhanced. As America's original super soldier, the Captain is appalled to suspect that the violent, musclebound, insane man with little regard for the lives of civilians, appears to be the country's latest super soldier. Unsatisfied with the evasive answers given to him by Nuke's superiors, he breaks into the base's computer files to discover more about Nuke. He turns out to be the only surviving test subject of a severely flawed attempt to recreate Project Rebirth, the same project that originally enhanced the Captain's own body.
Enraged by the treatment he is receiving in the media, Nuke breaks free from custody in the same base and runs amok in an attempt to attack the offices of the Daily Bugle. He's stopped by the Captain, but nonetheless, the military attempts to kill him, as do the Kingpin's men; however, though mortally wounded, Nuke does not die immediately. Daredevil first attempts to get him to a hospital, but realizing that Nuke will not survive, he then decides to get him to the Bugle instead in an effort to prove that Nuke is a government operative and that his presence in New York is the product of the Kingpin's widespread influence in the military.
In the end, the Kingpin's public image as an honest and respectable businessman and pillar of community is shattered, although he manages to avoid imprisonment while he plans for his revenge on Murdock. For his part, Matt Murdock accepts and enjoys a new, different but apparently fulfilling life in Hell's Kitchen with Karen Page and expresses no regret over the loss of his previous lifestyle as a successful lawyer.
"Daredevil: Born Again" deals with a number of themes, but the one central to the story is personal integrity in the face of corruption.
Murdock himself is portrayed as a powerful, honest man who is nonetheless driven to and beyond the brink of insanity by the machinations of a thoroughly corrupt individual; yet a purity of spirit and supreme willpower eventually win out. Uncompromising integrity is not an unusual theme in Miller's work, yet it's rarely been portrayed as powerfully as here. The Kingpin annihilates Murdock's life with such an efficiency that he literally has nothing left, not even his own sanity; yet he cannot stop moving, fighting and struggling to get back up. This theme is also seen in the character of reporter Ben Urich, who – despite getting his fingers broken by the Kingpin – in the end refuses to stay quiet and continues to write exposés about the crime lord, even when his wife becomes the target of an attempted murder.
Like much of Miller's work, "Born Again" has a strong political content, even though it reads more as a tale of personal redemption. Captain America is portrayed as a man out of place, the spirit of America from an ostensibly more straightforward, honest, and fair era. Nuke, on the other hand, is a Rambo-like figure: a musclebound, drug-fueled, easily-manipulated fanatic who murders civilians and destroys property indiscriminately -- all in the name of blind 'patriotism', while disdaining the nation's media and citizenry. Published during the Reagan administration, at a time when the Vietnam War and war veterans were still a very current topic, "Born Again" was very much a contemporary work. Miller's portrayal of the 1980s embodiment of the American Dream – a brainwashed and violent man who routinely murders civilians and is constantly used in various clandestine black operations in other countries – stood in stark contrast to a more traditional and pure-hearted, tired old man who nonetheless perseveres despite the odds.
Miller's treatment of the superhero team the Avengers was also somewhat unusual for its time. The superhero group only appears very briefly, during the climax of Daredevil's battle with Nuke. While the group's appearance lasts only a page-and-a-half, it makes an impact precisely because its presence is so brief. The team take control of the situation with seemingly god-like ease, far removed from the humans it saves: Thor is depicted as an impersonal elemental force — an actual God of Thunder — rather than merely yet another superpowered man; Iron Man is not so much a man in a metal suit, as he is a humanoid machine capable of razing entire cities; and, leader Captain America is the ultimate soldier and incarnation of a nation's spirit. While portraying superhumans as almost frightening and somewhat inhuman beings has since become far more commonplace, it was an unusual image in a mid-1980s, mainstream superhero comic. In comparison to the Avengers, Daredevil appears as a vulnerable human figure — indeed, he spends most of the storyline out of his costume.
Miller and Mazzucchelli dedicated the final chapter of the saga to Jack Kirby. Kirby at the time was engaged in a bitter dispute over the copyright of his work with Marvel Comics.
The nightstick with which Fisk had the cabbie beaten with makes a brief reappearance in a later story. In Daredevil #300, the climax of "The Fall Of The Kingpin" story, the tables have turned for Fisk -- Murdock is now the one systematically destroying Fisk's business and image, while Fisk struggles to hold on to whatever he has left. As an act of desperation, he goes to the New York Port Authority Terminal, where he had the nightstick -- complete with the blood stains of the cabbie and Murdock's fingerprints -- stashed away. In a flashback to the scene where Murdock is in the cab being pushed into the river, Fisk claims that it's good to hold on to such incriminating evidence, as someone might want to resurrect Murdock's fallen image.
Daredevil tracks Fisk to the terminal. Fisk, seeing Daredevil behind him, loses his composure and smashes his way through protective glass to retrieve the nightstick. He then flees through the terminal in a chase photographed by Peter Parker, who is confident enough that his friend has the situation well enough in hand to not interfere. Daredevil follows Kingpin to a nearby lot where some homeless are warming themselves over a fire they started in a barrel. Daredevil manages to wrest the nightstick away from Kingpin and toss it into the fire, causing any incriminating evidence that Kingpin might have used against Murdock to be destroyed.
In an ironic twist, the story ends with Kingpin confronted with a low-level mob contact who feels the time is ripe to take Fisk for whatever he's worth left -- including having Fisk retrieve his laundry for him. Fisk, enraged, smashes the man's skull in with his cane, walking off with a renewed sense of purpose. Much like Murdock, he intends to fight his way back from insanity and homelessness through sheer willpower. Meanwhile, Murdock is readmitted to the bar and resolves to continue his protection of the innocent as Daredevil.