What could possibly be more awe-inspiring than the sight of Thor, God of Thunder, clearing the crisp autumn air, propelled by the mystic mallet, Mjolnir? Little, perhaps, save for the sight of that selfsame deity cleaving the crisp autumn air with an island in tow! For months, the man-made island known as Hydrobase has served as the headquarters of the world's mightiest team of heroes while floating somewhere in the Atlantic Ocean outside US territorial waters. Now, after weeks of negotiations, the Avengers have secured permission from the Port Authority to permanently moor the mountainous barge to New York Harbor. And with its recent purchase from the US Oceanographic Institute, Hydrobase has been officially rechristened Avengers Island!
Thor pulls the island past the Statue of Liberty, while choppers fly by to get a close view of the action. At the fore of the island stand three of the five active members of the Avengers – Susan Storm-Richards a.k.a. the Invisible Woman and Reed Richards a.k.a. Mr Fantastic, both former members of the Fantastic Four, and Steve Rogers a.k.a. Captain America, the Avengers' new chairman. Invisible Woman holds some blueprints up with an invisible force field, while Reed stretches his arm out and points at a location on the map and tells Cap that with the base closer to the city, it will be a lot more accessible, particularly once he installs the transport shuttle tube from Battery Park. Reed tells Susan to keep the blueprints steady with her force field. Cap tells Reed that he thinks it was a good move, as normalizing relations with City Hall can only make things run more smoothly for the Avengers.
Cap thinks to himself that Reed has been extremely helpful in the various projects he has undertaken since assuming leadership, but wonders if Reed misses being in command.
Reed then announces that their instruments show they are in the designated position, and reports that he will signal Thor. Cap watches as Reed extends his arm upwards, and thinks that Reed's stretching ability and Sue's invisibility and force field powers are going to be an asset to the team. Thor notices Reed's arm stretch right up to him and gives him the “thumb's up” signal. Thor smiles and remarks that it is his time to being descent, and as he drops down to Avengers Island, holding the larger cables that he was using to tow the island, Reed tells him that he did good work, bur that there is more to do, and he and Gilgamesh now have to pound the mooring shafts in yet. Thor reminds himself that Gilgamesh a.k.a. the Forgotten One, is one of the strange off-shoot of man called Eternals, who has of late come to call the Avengers home.
Reed tells Thor that he better move it, or it is all liable to float away on them. Reed picks up a radio transmitter and contacts Gilgamesh, authorizing him to pound his mooring post into the ground, and not to worry about damaging it, as it is made of indestructible adamantium. Nearby, Gilgamesh holds the massive adamantium peg over his head and as he prepares to slam it into the island, he thinks that this is merely a laborer's task, but that it still has the seeming of a great feat – the kind of exploit he performed endlessly in the ancient days, when his deeds shock the world of humans – and legends grew in his wake. Gilgamesh then slams the large adamantium peg into the island.
Cap, Reed and Susan find themselves approached by two others, Edwin Jarvis, who excuses himself for the interruption, before introducing the Avengers to Michael O'Brien. Cap shakes Mr O'Brien's hand. 'tis a pleasure – no, an honor, to be here, Sir' Michael tells Cap, who replies that the pleasure is all his. Cap introduces Michael to Mr Fantastic and the Invisible Woman, and informs his new teammates that Michael used to be head of security at Project Pegasus, and he has hired him away to do the same for the Avengers here at Avengers Island. 'It's an honor' O'Brien remarks as he shakes Reed's hand. Cap then walks towards the Avengers' HQ on the island with Jarvis and O'Brien, who asks Cap if he is hiring a full team of specialists to run things for him. Cap confirms that, and explains that Jarvis will coordinate everyone.
Susan turns to Reed and asks him if he has noticed how business-like the Avengers are run compared with the Fantastic Four. 'Hmm?' Reed replies, without looking up from his blueprints. Sue then asks her husband if he has considered how long they will stay on as members of the Avengers. Reed informs Sue that the challenges of helping Cap get his group back on its feet interest him more and more, but that he hasn't decided how long to stay. Sue looks at her husband and thinks that she knew it was too much to hope he would stay retired from super-heroing any longer, and wonders whether Reed is trying to make his mark in this team because his best friend, Ben, is doing so well running the new Fantastic Four. 'Who would have believed those two could ever be in competition?' Sue wonders.
Suddenly: 'Reed! Over there!' Sue exclaims as she sees a large blazing A appear over New York City. 'What in Heaven's name?' Reed wonders as he looks over. They rush to their Fantasti-Car which is parked nearby and Sue wonders if that could be her brother, Johnny, trying to signal to them, possibly needing their help. Reed tells Sue that he doesn't believe the Human Torch would expend so much flame-power just to get their attention, and suggests they have the other Avengers investigate with them.
And soon, Cap and Gilgamesh sit in the back of the Fantasti-Car as it flies over New York City, with Thor flying alongside them. Reed reports that the fiery symbol appears to be emanating from somewhere near Central Park, to which Thor points out that is somewhere quite familiar to the Avengers. As the Fantasti-Car descends, Cap points out that the signal is coming from Fifth Avenue and 71st Street – where Avengers Mansion used to be, and adds that when they moved to the island, they had their old property turned into a park. Cap leaps from the Fantasti-Car and Thor moves down alongside him as Cap sees a figure with a smoking baton – the erstwhile Avenger known as Starfox. Thor recognizes Starfox and asks him if he is injured. Steam rises from the baton that Starfox is holding as the Eternal reports that he is alive, and lucky to be.
The Avengers all gather around Starfox, who tells them that he came to Earth to warn them. 'He's coming! He already beat Firelord! But I have his baton here!' Starfox utters, as Cap realizes Starfox used the baton to make the giant “A”. Starfox explains that he and Firelord were pursuing his grand-niece Nebula in space, for crimes she committed, then they encountered a being who calls himself Super-Nova – the last survivor of the planet Xandar! Starfox reveals that he is so powerful, he defeated Firelord. 'And I barely escaped to come and warn you' Starfox adds. Cap recalls Xandar as the planet that Nebula recently destroyed, and wonders if Super-Nova is out for revenge on Nebula. Thor recalls that using base sorcery, Nebula even wiled her way into the Avengers for a time, to which Starfox realizes that while he and Firelord searched the stars for her, she was here on Earth all along. 'What irony!' he exclaims.
Reed reports that her has been to Xandar and met members of their Nova Corps. He asks Starfox if Super-Nova is one of them. Starfox assumes so, and reveals that Super-Nova has the power of the entire Corps combined, and is on his way to Earth. Starfox struggles to get up, so Cap tells him to take it easy, and that they will get him to a doctor. Thor points out that Starfox's alien physiology will only confound a mortal physician, but he knows one who can assist, and picks Starfox up in his arms. Reed asks Starfox if he can indicate from what direction Super-Nova will be coming, and pointing upwards Starfox replies that her will give the coordinates as best he can.
One hour later, the Fantastic Four's specially designed ICBM lifts off from the Fantastic Four's headquarters at Four Freedoms Plaza. Aboard, are the current Avengers, sans for Thor who is flying towards the rocket, thinking to himself that since Starfox has been put to bed, he can join his fellow Avengers. Thor notices the airlock has been opened in the rocket to receive him, and once inside, he approaches Reed, Sue, Cap and the Forgotten One who are in the main cabin. Thor reports that his physician friend indicated that with care and rest, Starfox will recover fully. 'That's great to hear' Cap replies, before telling Thor that he wonders if his physician buddy would like to be put on retainer as the Avengers' official medic. Thor assures Cap that when they return he will ask him.
Reed reports that he is scanning nearby space for any unaccounted mass in the general vicinity Starfox mentioned. Cap looks around the rocket, and thinks that he always thought the Avengers' Quinjets were sophisticated, but this is some ship. 'Heads up, people! The instruments are onto something!' Reed announces, while Sue maintains a force field around Firelord's baton, pleased she thought to bring it along, for if they find him, Firelord may need it. Suddenly, a large spaceship comes into view. 'Look at the size of that ship! Even our rocket is dwarfed by it!' one of the Avengers calls out, while Reed remarks that it looks vaguely Xandarian in design, but he can't figure out why the ship isn't cloaked, as the Xandarians have that technology. Sue suggests that perhaps Super-Nova is arrogant in his power and wouldn't bother. 'Arrogance has proven the undoing of more than one tyrant' Gilgamesh reminds his teammates.
The rocket lands on the surface of the large spaceship and Reed points out that with his superior technology, Super-Nova will have seen them long before they came across the spaceship, but he didn't fire at them, so if he is arrogant enough to remain visible, he may also be arrogant enough not to perceive them as much of a threat. Reed suggests that they try to board the other vessel, and as the team put on some strange spacesuits, Reed tells them not to let the fact they are transparent fool them, as they are made of Unstable Molecules and can easily withstand temperatures – he doesn't get to finish his sentence as Cap interrupts him, telling Reed that they get the picture.
The Avengers find their way into the enormous vessel and go into free fall. Reed tells his teammates that there is apparently no gravity mechanisms in here and asks Sue to to put a force bubble around them all so they can move as a unit through the ship. Cap and Thor are further ahead, and Gilgamesh is some distance back from Reed and Sue. Sue tells everyone to try and come together for a moment, and once they do, she encases them all in an invisible force field. Cap finds it interesting that Richards takes over and starts giving orders, even though he is Avengers leader, before deciding that since space is more Reed's domain than his, he is sure there is no slight intended. As the force bubble floats through the vessel, Gilgamesh asks Thor if Starfox mentioned anything else to him about what to expect up here when he took him to the doctor, but Thor replies that he didn't, and that the battle with Super-Nova took place in space, not inside the ship. 'If indeed this is the Xandarian ship' Cap remarks. Reed holds Firelord's baton and tells Cap that he believes this is the Xandarian ship, as Firelord's baton is glowing more brightly, so they must be nearing him – unless this is a trick.
'OMIGOD – LOOK!' Susan shouts as she sees something up ahead. 'What -?' Cap asks, as dozens of what appear to be brains fly towards the force bubble. 'They're brains – brains flying towards us!' Sue gasps, suggesting that perhaps this isn't the Xandarian ship and this bizarre life-form might be what is in command here – it might not be an attack. Thor tells Susan that they cannot take that chance, and raising Mjolnir, he declares that they must strike first, or mayhap they will be overwhelmed by superior numbers. 'Thor – don't!' Reed shouts, as Thor releases Mjolnir, Reed stretches out to grab it – but misses. 'Listen to me, Avengers – you'll hit the force shield! You'll -' Reed calls out, before telling Susan to drop the field, as they can't have the hammer ricocheting around in here, they will have to chance an encounter with these strange creatures.
Sue suddenly releases the force field, telling herself that she might have held it, but the strain was incredible, while Mjolnir slams into one of the brains, while the others latch onto the Avengers. 'You still think these fiends may be of benevolent nature, Invisible Woman?' Thor asks. Cap blocks several brains with his shield, while thinking that this was a foul-up they could have avoided, but they still have a long way to go before they are not stepping on each other's toes.
For a seeming eternity, the Avengers seem crushed within the ever-increasing gelatinous mass of brains, then, suddenly, the brains a scattered apart as Gilgamesh swats his way through them, boasting that h will never surrender to such an ignoble fate. 'If I perish, it will be at the hands of a warrior-born!' Gilgamesh exclaims. Thor agrees, and as he slams Mjolnir into one of the brains he declares 'Let these space-spawned scum know 'tis the Avengers they have attacked with impunity! The Avengers!' Reed notices what happened to the brain that Thor destroys with his hammer and tells the other Avengers that the dismemberment of the brain shows that the “nerve” connections are electrical, not organic, so they needn't worry about killing them – at best, they are “pseudo-life”. Sue struggles against the brain that wraps a tendril around her neck, strangling her, so she attempts to project a force field inside the brain, then expands it, blowing the brain apart.
Cap uses his shield to shatter one of the brains, but as he and the others continue to free fall, he realizes that they are holding their own, but cannot brace against anything, and that only Thor seems comfortable with the conditions. Suddenly, two brains latch on to Gilgamesh's head, and he cries out, 'Reaching inside!' he warns his teammates, before reaching around with his hands, pulling the brains off of his head and slamming them together, shattering them. 'Off, villains! You'll not make a meal of me! But you may dine on each other!' Gilgamesh calls out. Thor knocks his foes back by spinning Mjolnir around, creating a vortex, and as he stretches his form between the various brains, and uses the baton to keep them at bad, thankful for the fact that the Avengers are getting the advantage on these bio-mechanical monstrosities. Reed thinks that if Thor hadn't acted so rashly, they might not have had to fight so quickly.
The tide of the battle moves irresistibly towards Earth's Mightiest Heroes, as the swat and cut their way through the brain leeches, while continuing to free fall. Reed stretches his body as what appears to be the last contingent slams into him. He plans to scoop them up, then scatters them, sending them careening throughout the ship. The remaining brain leeches start to flee, and Cap instructs Gilgamesh to let them go. 'But, Captain – my helmet! One of the creatures ripped it from me! I must -' Gilgamesh calls out, but Cap tells him that he doesn't care, and to get back with the rest of the group. Cap thinks to himself that the Avengers may have won, but it wasn't as a team, it was as individuals. He knows that he has to forge his teammates into a fighting unit, and hopes that they get through this escapade without stumbling too badly. He realizes that they may not get a second chance.
As they are still in free fall, Reed stretches out his arms, and takes Gilgamesh with one hand, and Cap with the other, pulling them in closer. Susan asks her husband what he thinks those creatures were, to which Reed announces that he thinks they are components of the Xandarians' living computer, which he once saw, and supposes that they must have been the mechanisms by which the brains of deceased Xandarians were preserved. Reed informs Sue that they need to bring with them a reasonably intact specimen and suggests to her that an auxiliary force field should do it.
Moments later, the Avengers continue to float through the ship inside one of the Invisible Woman's force fields, while one of the brain leeches floats alongside in another force bubble. Reed notices that Firelord's baton glows more brightly as they move through the ship, which means they are getting closer to Firelord. Cap decides that Reed is intent on being the scientist, no matter the circumstances. Cap plans to let it ride for now, but knows that Reed's priorities are a little off, as this is not a research expedition. They move into another part of the ship and the flare of the baton gets brighter, so Reed assumes that Firelord must be through the next airlock – and as they pass into the next part of the ship, they indeed come across Firelord, strapped to various cables that suspend him from the ship. Reed sees the wires and electrodes and tells the other Avengers that they can't just rush in and effect a rescue.
Reed instructs Sue to slow drop her force field when he gives her the order, as he plans to extend Firelord's baton, and hopefully his hunch will pay off. An instant later, energy pours from Firelord's baton, engulfing Firelord and the cables that restrain him. 'Richards – are mine eyes deceived or have you used Firelord's very weapon against him?' Thor asks 'What can this mean?' Gilgamesh enquires, while Reed tells everyone not to panic, explaining that he merely released Firelord from the web of electrodes, despite what it looked like. Cap tells Reed that, as leader of the Avengers, he would appreciate being advised of any dramatic actions on his part. 'Oh...of course, Cap. Sorry' Reed replies, before he stretches over and grabs Firelord, as Cap asks if he is alive. Reed confirms that he is, and explains that he surmised from discussions with the Silver Surfer that such a weapon containing the power cosmic would probably not harm its wielder, and would actually act on his behalf. Reed admits that there are exceptions, but tells his teammates that he channeled the power carefully.
Thor declares that Firelord was a noble ally, and sometimes foe, and he rejoices that Firelord lives, before announcing that they need to seek the base villain who put him in such an ignominious state. Suddenly, the Avengers turn as a burst of light shines behind them. Cap tells his team to look sharp, as this may be the showdown. They look up in awe, 'No wonder Firelord didn't stand a chance!' the Invisible Woman remarks. 'But we stand together – and will prevail!' Gilgamesh boasts. 'By Ymir's beard!' Thor gasps – as the mighty Super-Nova looms over them, 'WHO DARES?' he booms. 'WHO DARES DISTURB THE SANCTUM OF THE LAST SON OF XANDAR?' he asks to which Thor boasts 'We do, villain! We – the mighty Avengers dare disturb thee – and more!' 'The Avengers! What fortune smiles on me! I demand you turn over the Avenger called Nebula to me – now!' Super-Nova announces.
Cap informs Super-Nova that Nebula joined the team temporarily through trickery, but they know her to be evil, and that she is not with the Avengers. Super-Nova replies that he will not be the victim of such obvious deception, and states that the Avengers seek to hide her from his wrath, realizing that the other fool who appeared with Firelord and escaped must have warned them. He tells the Avengers that because they refuse to surrender, he shall journey to their Earth and devastate it until Nebula is given to him. Thor begins to spin Mjolnir, 'Verily, thine arrogance is exceeded only by thine ignorance!' he calls out, assuring Super-Nova that Captain America speaks the truth, as Nebula is not among them on Earth. 'But if still thou seeks battle – the Avengers stand ready!' Thor warns Super-Nova.
However, Super-Nova announces that he has no time to engage in pointless struggle with such inferiors, as other pursuits now engage him. With that, Super-Nova begins to glow and vanish. 'Nothing can stop what's happening!' Reed calls out, horrified, 'He's about to go – super-nova!' Reed warns the others, as Super-Nova indeed blasts from the spaceship, into space, energy crackles and booms around him and the spaceship as he boasts that he will ravage the Earth and leave it a smoldering cinder unless the woman called Nebula appears and vengeance is his!