Annihilation started with a 48-page one-shot issue entitled Annihilation: Prologue which was released on March 15, 2006 and then followed by four 4-issue mini-series: Annihilation: Silver Surfer (April 1 2006), Annihilation: Super-Skrull (April 12 2006), Annihilation: Nova (April 19 2006), and Annihilation: Ronan (April 26 2006). The event concludes with a 6-issue limited series entitled Annihilation, bringing the four stories together, and a Post-Annihilation 2-issue mini-series. The limited series Drax the Destroyer: Earth Fall (September 28 2005) was a prelude to the event.
Drax attacks the others to keep them from harming innocent lives. When he is seemingly killed by Paibok, a new body emerges from the remains, appearing to have lost some of his strength and resilience, as well as his ability to fly and shoot energy blasts.
However, his intellect has returned to its original level, and he has taken a liking to using knives in battle. He also takes the role of protector of a young Alaskan girl named Cammi whom he seems determined to protect at all costs. This Drax with a new body defeats his fellow prisoners. The limited series ends with Drax and Cammi back on a prison ship.
Death appears to be referring to the coming of a massive insectoid military force (the Annihilation Wave) through the center of the universe, known as "The Crunch," where the Negative Zone flows into our universe and increases its size. Which immediately sets to the destruction of the Kyln structures — artificial moons that serve as both galaxy-wide power generators and a death-row prison — that orbit the Crunch. The emergence of this force and the destruction of the Kyln are referred to in captions as "Annihilation Day."
The Annihilation Wave cuts a swath to the planet of Xandar, where it quickly destroys the planet's surface and wipes out all of the Nova Corps, leaving Richard Rider as the organization's only survivor.
The Prologue also shows the arrest of the Kree Ronan the Accuser in the midst of his duties; the Silver Surfer's realization of something being amiss; and the Super-Skrull in hiding on a Kree starbase. These segments serve as starting points for the four Annihilation limited series.
Four days after the Annihilation Wave struck Xandar, Nova wakes up to find out he is the sole survivor. In an attempt to carry them both to safety, Nova allows Xandarian Worldmind to install both the entire Nova Force and the Worldmind itself within his body.
He saves two other survivors of the attack on Xandar, Drax the Destroyer and his companion, Cammi. After bringing the two refugees to Nycos Aristedes, Nova then agrees to assist Quasar in protecting the fleeing inhabitants of that planet.
After Nova uses his power to open a stargate large enough to accommodate the entire planet's population, he and Quasar battle the Annihilation Wave in an effort to buy time for the refugees. With the combination of the Nova Force and the Worldmind's calculating capability, Nova puts up a good fight, but realizes that he will eventually lose.
Over the continued objections of the Worldmind, which wishes to retreat to safety to ensure its own survival, Nova and Quasar accept Drax's advice to ignore the fleet and attack Annihilus personally. Annihilus easily defeats them, stealing Quasar's quantum bands and energy (which kills Quasar in the process). However, Annihilus is sabotaged by the Worldmind when he tries to consume the Nova Force, and his fleet begins destroying itself. Made furious by this, Annihilus withdraws while Nova flees.
With the evacuation fleet safely through the stargate, Nova and the Worldmind agree that, rather than delivering the Worldmind and Nova Force immediately to safety, the two of them will remain united to fight Annihilus. Nova reunites with Drax and Cammi, and asks Drax for lessons in how to destroy.
Although Terrax's fate is unrevealed, Annihilus kills Morg in an unsuccessful attempt to drain his power. Several of the other former heralds, Firelord, Red Shift, and Stardust, decide to fight a war against the Annihilation Wave, while the first herald, the Fallen One, carries out its own mission for Thanos.
Ultimately, the Surfer elects to return to Galactus as his herald in order to help protect Galactus from Annihilus' attacks and preserve Galactus's role as a necessary element in the balance of the universe. The Surfer easily defeats an entire attacking fleet, as well as the Seekers' leader, Ravenous; but despite Galactus' insistence, the Surfer refuses to kill Ravenous.
In a side plot, Galactus reveals that the Annihilation Wave's destruction of the Kyln may have freed two Proemial Gods, Tenebrous and Aegis, that he imprisoned when "the universe was young." Thanos, guided by Skreet, a fairy-like "chaos mite", and by Death herself, allies first with Annihilus, then with Tenebrous and Aegis.
Ultimately, Kl'rt and a young Skrull engineer, R'Kin, travel to the Negative Zone in order to seek a method of stopping the Harvester of Sorrows, a planet-buster weapon, from destroying Zaragz'Na. In the Negative Zone, Kl'rt locates Hawal, the warden of a prison planet and designer of the Harvester, and tortures him into designing a virus that can destroy the Harvester and unites the planet's prisoners into an army.
As Kl'rt's fleet prepares to attack the Harvester, R'Kin volunteers to pilot the ship carrying the virus. Although Kl'rt's fleet fights bravely in order to create a diversion, the virus ship never appears. Disillusioned by the Super-Skrull's savage tactics and resentful over his own father's death in one of Kl'rt's earlier campaigns, R'Kin sells out Kl'rt to the Annihilation Wave, turning the virus over to Annihilus's forces unused. Kl'rt, along with Praxagora and Preak (two allies liberated from the prison) are captured, and Zaragz'Na is destroyed.
As R'Kin and the Harvester's commanders mock the captives, the Super-Skrull uses his rarely employed power of hypnosis to force R'Kin to free the three captives. Preak sacrifices himself holding off pursuers, while Praxagora heads to the center of the Harvester, planning to destroy the weapon at the cost of her own life.
Kl'rt captures R'Kin, who tries to bargain for his own life by proposing that the two of them escape from the ship, allow Praxagora to destroy it, then claim credit with the empire as heroes. Instead, the Super-Skrull traps R'Kin, leaving his limbless torso in a ship to die.
In the ship's core, Kl'rt decides that he will not sacrifice any more people for his cause. He absorbs Praxagora's near-infinite release of energy himself, allowing her time to escape the ship, then releases the energy, destroying the Harvester.
The series ends twenty years after the attack of the Annihilation Wave. In the epilogue, Praxagora is telling Kl'rt's story to a group of young Skrulls and explains that by making his sacrifice to destroy the Harvester of Sorrows, Kl'rt finally had become what he had always wanted to be: a hero.
Ronan lands on Godthab Omega, where he finds an encampment of exiled Kree, including his old friend Korath, and learns that Tana Nile has joined the Graces, a group of cosmically powered women led by Gamora. After defeating Nebula and Stellaris, Ronan ends up in battle against Gamora herself, who now possesses the power cosmic. However, in truth their conflict, as well as several others, are actually caused by the manipulation of Glorian, who is using the energy from their battles to attempt to reshape the world.
Just as Glorian's plan approaches completion, the Annihilation Wave attacks Godthab Omega. Ronan, Korath, Gamora, and Glorian all battle Annihilus's forces, while Tana Nile is killed in the battle, preventing Ronan from proving his innocence. Undeterred, Ronan resolves to return to the Kree, violating his exile to warn them of the coming danger.
205 days after Annihilation Day, Richard Rider has formed an army, the United Front, to oppose the Annihilation Wave. His land-based army includes Drax, Gamora, Ronan the Accuser and Peter Quill, while his outer space forces consist primarily of Firelord, Red Shift and Stardust. As Rider's ground troops attempt to retreat under crushing odds, Firelord attacks the enemy command ship, capturing their Queen and causing the enemy forces to collapse in confusion, at the possible cost of his own life. After inspecting Firelord's comatose body, Rider and Quill question the Queen, who reveals that while the United Front forces fought the Annihilation Wave, Thanos, Tenebrous and Aegis had already attacked and incapacitated Galactus and the Silver Surfer. Believing the Power Cosmic to be within his grasp, Annihilus orders his troops to kill the remaining former Heralds of Galactus.
Thanos kidnaps Moondragon and rips off her ear, which he sends to Drax to warn him that her fate is in his hands. Drax believes that Thanos wants him to stay away or he will kill Moondragon. Drax resolves to kill Thanos. Nova fights Ravenous, who returns with a series of others under his control. Annihilus presses Thanos for the result on how the power cosmic can be used biologically, which he will apparently use on Galactus, the Silver Surfer and Terrax. Thanos tells him that he will have the answer soon.
Nova and his allies battle the forces of Annihilus. During the conflict a huge energy spike restores the deceased Super-Skrull Kl'rt to his full power. In the aftermath of the battle Nova sends out a warning to the heroes of Earth about the cosmic conflict. Drax stays behind the battle lines as he tries to head towards the forces of Thanos to complete his mission once and for all.
Moondragon confronts Thanos, who reveals that he helped Annihilus merely to sate his curiosity as to how everything would play out in the end. However, it soon becomes apparent to Thanos that for once he himself has been played for a fool. Annihilus, feigning ignorance of the principles behind Thanos's Power-Cosmic-draining technology, has instead secretly reverse-engineered and reconfigured the massive device into a "Galactus-Bomb." If detonated, this will set off a chain reaction that will destroy the universe as well as the Negative Zone. Drax forces his way onto the Annihilation Wave ship on which Galactus is harnessed and where Thanos is attempting to activate a failsafe he had himself previously built into the device for just such a contingency.
Unfortunately for Thanos, his fail-safe is constructed in such a way that he cannot disengage from it once activated, nor can he stop or pause the process once begun. Drax locates and confronts the occupied Thanos and punches straight through Thanos's body, tearing his heart from his chest, as Death watches.
Drax is now free of the "madness" that has gripped him up until the moment that he successfully killed Thanos, and his daughter Moondragon is at last able to reason with him and inform him of the impending activation of the Galactus-Bomb; together they try to free Galactus themselves.
In the meantime, Ronan the Accuser and a small band of allies (including Ronan's sworn enemy, the Super-Skrull) arrive on the homeworld of Kree House Fiyero (the de facto ruler of the Kree Empire during the absence of the missing Supreme Intelligence). In the course of battle, it is quickly revealed that House Fiyero sold out to Ravenous and Annihilus; because of this, the Kree Empire did not field nearly as many troops against the Wave as would normally have been expected. Ronan almost single-handedly defeats the Royal Guard of House Fiyero and a small army of Ravenous' minions. After passing judgment on the ministers of House Fiyero, Ronan discovers that the ministers were in fact responsible for the Supreme Intelligence's disappearance, and lobotomized it against its will. Upon seeing this horror, Ronan puts the Supremor out of its misery. He emerges from the citadel to a massive throng of Kree, who unanimously call on him to become their new emperor.
Back on board the Annihilation ship, Drax uses Silver Surfer's Power Cosmic to fool Thanos' safeguards and frees the Surfer, who in turns frees Galactus. Drax and Moondragon are teleported by Galactus to one of the Kree worlds out of harm's way as Galactus proceeds to unleash a massive, omnidirectional blast that later becomes known as the "Galactus event." Silver Surfer is sent ahead of the blast by Galactus to herald the imminent destruction, as the unleashed "Galactus obliteration perimeter" wipes out the majority of the Annihilation Wave, more than three star systems and even vaporizes a Watcher.
Nova, Peter Quill and Phyla-Vell have teleported close to Annihilus' flagship and are preparing to make the last jump when Galactus' energy wave arrives. Annihilus, finding that he has been betrayed by Thanos and undone by Galactus, uses Quasar's quantum bands to protect himself from the energy blast. On the Kree homeworld of Hala, Ravenous' forces begin to attack from the atmosphere, and are met in quick violent battle by the Kree; led by Ronan, entire building complexes are rocket propelled at Ravenous' forces and decimate the Annihilation forces.
Annihilus emerges from the wreckage of his flagship as Galactus leaves. Nova arrives, having survived Galactus' energy wave as well as encasing Peter Quill and Phyla-Vell in an energy bubble. Nova and Annihilus fight. Phyla-Vell forces her way out of the bubble as Annihilus overwhelms Nova. Annihilus throws her aside, but the quantum bands abandon him and join with Phyla-Vell. Using this momentary distraction, Nova surmises that the gap in Annihilus' armor is his mouth, forcing his hand down Annihilus' throat and tearing out his insides. Both Annihilus and Nova slump to the ground as Nova looks up to see the veiled figures of Thanos and Lady Death looking over him and smiling. Nova tells them, "Better luck next time."
The remainder of the story is a summary by Nova to his Nova Corps verbal log explaining the series of events that followed after Galactus was freed and Annihilus was destroyed:
On Kree-Lar, former capital of the Kree Empire and now seat of the territories ceded to the Annihilation Wave, Ravenous oversees a birthing by one of Annihilus' Queens: a reborn Annihilus.
Two issue limited series featuring two stories each issue, the first issue features Stardust and Terrax, the second features Firelord and Silver Surfer.
In Terrax, after being captured, enslaved and made a pawn of Annihilus, Terrax has broken free...only to crash-land on a planet ruled by the Space Parasite. He decides to destroy this murderous entity as a way to regain his honor.
In Stardust, Stardust returns from death and re-devotes himself to Galactus.
In Silver Surfer, the Silver Surfer chases down Tenebrous and Aegis, the two Proemial Gods who recently defeated Galactus.
In Firelord, Firelord tracks down many of the Centurians--Annihilus's elite force that murdered his homeworld and many other worlds. He kills some, but others plead for mercy, saying they were tricked. Firelord allows them to live, but only if they behave from that moment on.