The series follows the last days of the New Gods as they are stalked by a mysterious killer.
In the same interview, he stated that: "They started building [the weekly series] Countdown around Death of the New Gods because it was way ahead of everybody else. They started catching up with me, and I'm having to change my ending to adjust to what they're doing in Countdown. Up until now, I've been telling everybody I'm killing them all. One survives. And he was going to have a good death. I had to keep him around until the end."
The series starts with Darkseid recalling how he first became aware of a growing crisis with the Death of Willie Walker. Walker, who is the corporeal form of the Black Racer, is seen being killed by an unidentified figure who tears out his heart; the same fate that had met all the other New Gods who were killed. Orion, Himon, and others discover the full extent of the death toll when on screens shows the New Gods who have been killed and others who are still missing. Forever People are shown to be missing and are prime suspects as Serifan and Beautiful Dreamer are both seen leaving two of the murders. Orion blames Darkseid. Takion asks him to hold off until further information can be revealed. The Justice League comes to investigate Barda's murder. Dr. Mid-Nite performs an autopsy which doesn't reveal how she was killed. Mr. Miracle contemplates using the Anti-Life Equation to bring his wife back, but stops himself. He receives an urgent summons back to New Genesis. Superman and Mr. Miracle bring Barda's body back to New Genesis. Darkseid asks Desaad to investigate these murders by having him examine Justeen who was also murdered. Superman and Mr. Miracle arrive on New Genesis. Orion is insulted by Superman's presence and attacks him. Metron arrives and reveals what the cause of death is to all the New Gods. Darkseid has also come to the same conclusion: their souls have been taken from them. Darkseid wonders if all his theories on the Anti-Life Equation were actually true or not.
While searching the Wall for clues, Takion is killed by a mysterious assailant whom he recognizes. Superman, Scott Free and Orion battle Darkseid's shadow demons, and discover that Darkseid has obtained a portion of the Anti-Life Equation, which is still not as strong as Free's full control. Stalemated, Darkseid tells the heroes that he knows what is causing the murders, but that even knowing that he will die, he sees a chance to gain advantage, though he'll still not reveal his plot to the three heroes.
Superman, Orion, and Mr. Miracle discover that the Forever People have been murdered as well. Free resurrects the Forever People and demands that they tell him who has killed them. While each one recounts his or her death, Big Bear mentions that the killer was "the last person we'd expect to see". They disintegrate before they can tell Free anything clearer, claiming that they have been ordered not to reveal the secret.
In the past, Metron speaks to the glowing ball of light, which reveals itself as the Source and the cause of the death of the New Gods. Long ago, the Source was attacked by the Old Gods and split into two, light and dark. The light side recovered and brought about the Death of the Old Gods, and then attempted to recreate existence, but could only manage to make the flawed Fourth World due to its imperfection. It attempted to reunite with its darker part but was delayed by the events of Crisis on Infinite Earths, which unified alternate realities and created an impenetrable Source Wall. The Source then orchestrated the events of Infinite Crisis , apparently subtly manipulating Alexander Luthor, and later the events of 52 to bring back the Multiverse, and freeing its dark half which had taken the form of the Anti-Life Entity. The Source thus reveals that it is now using an agent to eliminate the Fourth World in order to bring about the Fifth World, which will be perfect. The Source agrees to Metron's request that he be allowed to witness the end of the Fourth World.
On Apokolips, Darkseid reflects that everyone is making a mistake in not paying attention to what he was doing, and that it would prove catastrophic. As he broods, images from Countdown to Final Crisis are displayed on the screens around him.
The reunited Source reveals how Miracle's beliefs were not of its doing. Miracle, feeling manipulated and betrayed by the Source, requests to be killed and he's killed off. Disgusted at the Source's ruthless treatment of its most loyal follower, Metron demands to be killed as well and The Source delivered Metron's request. The Source travels to Apokolips to engage the last New God, Darkseid, who has taken a serum giving him access to the power of the Anti-Life portion of the Source.
The Source and Darkseid battle as Superman watches on. Darkseid reveals that the Source's plan was to wipe out the New Gods and create the Fifth World. The Source then releases Orion's ghost to attack Darkseid, who flees. The Source merges New Genesis and Apokolips into one planet to create the Fifth World. Superman witnesses all of this and returns home, vowing to never forget the friends he lost. This series was conceived and created after Seven Soldiers of Victory, yet is connected to Final Crisis. Some of these connections are not clear as of yet. Orion's revival as an agent of the Source and his subsequent killing by a time bullet are part of the ongiong story to be revealed in Final Crisis. Grant Morrison scripts both Seven Soldiers and Final Crisis.
However, some of the dead New Gods have been returned to life, chief among them Darkseid.
DC's second weekly limited series Countdown ties into the Death of the New Gods limited series in several issues; after a battle in the clouds above Metropolis, Lightray was killed in Countdown #48 by the mysterious God-Killer, with his last words being "Infinite... Infinite...." Sleez was killed in #46 by the God-Killer, who proclaimed "So Begins The End!" as he blew a hole through Sleez; the Deep Six were all slaughtered in Countdown #38. The new Forager investigated the murders at the request of New Genesis, and later visited Earth to recruit Jimmy Olsen to help her after the death of Big Barda. In Countdown #19, Bernadeth was confronted by the God-Killer. In Countdown #10, Granny Goodness is killed by the God-Killer, once more.
The effects were also felt in other DC titles. In Birds of Prey #109, Knockout was killed, by a figure whose silhouette precisely matches that of the elusive New God, the Infinity Man. In the Outsiders - Five of a Kind: Thunder/Martian Manhunter one shot, Speed Queen of the Female Furies was fleeing from the God-Killer when she met a comatose Grayven, son of Darkseid. She was killed, though he escaped. Later, Grayven was tricked by the Martian Manhunter into returning to Apokolips, where he was killed as well. In Superman/Batman #42, Orion's wife Bekka was killed by the assassin. In Wonder Girl #5, while battling the novice Amazon Bloody Mary is killed.