JFK International Airport:
Three men within a small private plane are impatiently waiting for the Tower to give them permission to take off. They are extremely nervous, as well as they should be, considering they are evil scientists, members of the terrorist organization called the Enclave and are smuggling a mysterious crate to their new retreat. One of them, Shinski, remarks that they are being kept here far longer that traffic would require. He fears the authorities may be closing in on them. While one of the others, Zota, chides him for being paranoid, the third one, Morlak, alerts them to the police vans heading for them. Panicked, Zota starts the plane over the Tower’s protest: they are just about to crash into a Boeing 747!. Desperately, Zota pulls the jet into a sharp banking turn. Hopelessly out of control, the plane skids across the runway and into the waters of Jamaica Bay. In seconds, three quarters of its ruptured hull has sunk beneath the waters. The FBI agents getting out of the police vans watch in amazement as, suddenly, an energy geyser erupts from Jamaica Bay next to the plane. What was on the plane? they wonder.
The Avengers are in a heated video discussion with their government liaison, Raimond Sikorksi, who is horrified about their recent decision to include Namor, the Sub-Mariner, in their ranks. Cap appeals to Sikorski that now they have the chance to change Namor’s poor relations with the surface world and reminds him that Namor’s father was an American citizen and that Namor helped defend America during World War II. The Wasp chimes in, pointing out that their security clearance is in limbo, meaning the federal government has no say in what the Avengers do. They didn’t even have to inform Sikorski, but did. Sikorski protests that he has been working for weeks on restoring Avengers priority. Cap and Wasp both assure him that the Sub-Mariner will work out, while the Black Knight, admiring the way the Wasp handles the situation, wonders if he shouldn’t ask her out.
Three levels above, Captain Marvel and Hercules are showing Namor around the quarters. Namor scoffs at the ‘common hall.’ Opening the first door, he find a spacious room, decorated in a Graeco-Roman style very much to his liking. He announces that it will suit him fine. Unfortunately, it already belongs to Hercules. As the two men get into an argument, Captain Marvel switches to her lightform and takes off. Breaking up another fight between those two she doesn’t need.
Atop a high skyscraper roof, Monica wills herself back to human form. She sits down, wondering whether including Namor in the team is really such a good idea. As she looks across the city, she to sees the energy eruption coming from Jamaica Bay. She switches to her lightform and, a moment later, she is at JFK airport, joining the police and firemen.
The FBI agent in charge introduces himself as Derek Freeman and tells her how some fugitives, whom they believe to be Enclave members, crashed into Jamaica Bay. Captain Marvel remembers the Enclave, with whom the Avenger recently clashed, and asks if they are still alive. Freeman tells her they are, though they are in pretty bad shape. They are not his problem, however. They don’t know what cargo they had on their plane but, seconds after it spilled into the bay, the energy geysers started erupting every few minutes. He’s sent a couple of divers down.
At that moment both divers seem to be forcefully thrown out of the water. One of the divers, Nelson, explains that they found … something, apparently the source of that crazy energy. When the other man poked it with a probe, there was a voice unlike any they’d ever heard before. It warned them to keep away, then something grabbed them and threw them out.
Captain Marvel switches into energy form and flies to explore the waters herself. She finds a busted-up crate, the shattered remains of some glass tank, leaving her to wonder whether it was shattered on impact or if something broke out of it. She notices another light source and finds something looking like a dirty, giant cocoon, from which some energy emerges. Captain Marvel transforms her light energy into a stream of X-rays, intending to pierce the surface of the cocoon. Suddenly, though, she hears a voice in her head, warning her to keep away. Not only are Monica’s rays repelled but somehow, against her will, she’s also being turned physical. The voice keeps on shouting at her to leave it alone, while Monica is stuck in physical form and caught in the force’s grip. Suddenly, though, the force weakens, allowing Captain Marvel to swim to the surface.
Elsewhere, a gloating villain named Melter spies on the Avengers’ plane heading for JFK airport, thanks to the surveillance camera he had planted in their mansion. His henchman, Keegan, asks what good that camera will do them. As Melter impatiently rants about his plan to destroy the Avengers, he opens a closet to get something from it. Instead, he finds the body of the real Keegan inside. He turns around to find the impersonator holding his own weapon. Justice is served, the Scourge announces, as he kills another villain.
In the meantime, the Quinjet lands at JFK and the rest of the team joins Captain Marvel. Captain America draws a sketch of the cocoon after Captain Marvel’s description and asks her if it looked like that. After she agrees, he tells her he was afraid of that. He explains that, on at least two previous occasions, the Enclave had tried to genetically engineer a race of superbeings… both times involved cocoons like the one Captain Marvel described. According to the Fantastic Four, the experiments yielded Adam Warlock and the mystery woman known only as Her. Both rejected the Enclave’s attempts to subvert their will, but who knows how this new being down there will develop?
Wasp agrees and considers Cap’s words. Not waiting for her decision, Namor dives into the water. After all, underwater menaces are his specialty. While the team bristles at his rashness, Namor is suddenly being thrown out f the water, same as the divers before him. Wasp reads him the riot act and reminds him that he is part of a team now. The Avengers discuss their next step and Captain Marvel decides to fly to the hospital to pump the Enclavers for information.
Moments later, the rest of the team, having donned diving equipment, dive down. Cautiously, they surround the eerie cocoon, whose energy flickers through its rips and tears. Placid one moment, it lights up the next and the voice orders them to keep away.. Hercules tries to hit it and is struck himself by a force beam from the cocoon. Black Knight finds that, despite his sword’s capacity to deflect power beams, it cannot affect those blasts at all. Namor, Cap and Wasp find themselves surrounded and paralyzed by the light.
At that moment, miles away, Captain Marvel addresses professor Shinski in his hospital room. She asks him to tell her everything about his creation at Jamaica Bay, because then the courts may go easier on him. Shinksi doesn’t know what she’s talking about. When she mentions the cocoon, he decisively tells her that there was no cocoon in the crate. He and his associates were almost killed by previous cocoon creatures. They know better than to repeat such an attempt. The crate held Shinski’s new discovery in a glass tank, but the compounds would have been rendered harmless in the waters. He drifts off and Captain Marvel finds that she believes him. But where did that cocoon come from?
Back at the bottom of Jamaica Bay, Hercules is slowly making headway against the force pushing him away, much to the anger of Namor, who feels humbled by the Olympian’s superior strength. Cap notices that the force bolt only stops his forward movements. As he falls back, it fades out. But Hercules still makes headway and, as he does, the cocoon is slowly forced back shedding a coat of silt as it moves. Suddenly, the Avengers realize: the debris of the plane is still clean. It takes time for that much silt to gather on an object, so the cocoon was here before the plane crashed. Captain Marvel joins them to confirm their suspicions. Hercules moves still closer to it and, suddenly, they hear the voice again begging them to stay back. Wasp tells Hercules to back off, realizing that the voice sounds afraid.
Wasp wonders if the thing was just reacting to being jostled and probed and was therefore acting in self-defense. She slowly walks towards the cocoon and concentrates on it, thinking that they don’t want to hurt it; they want to help. Help? the voice repeats before asking Jan to please help. Jan tells the others to come closer. The voice fades but, suddenly, the cocoon’s outer cover peels off, leaving behind a clean smooth white capsule.
The Avengers take the capsule with them and try to examine it at Avengers Mansion. The Black Knight can’t tell the others much, except that the outer cover was just part of an old mattress somebody dumped. The capsule itself is something like a stasis field but it doesn’t act like any he’s ever encountered. And they’ve heard nothing more of the voice so far.
Captain America adds that he has checked with sources in the intelligence community, but nobody knows anything. He knows though that there was a space shuttle crash in Jamaica Bay a few years ago. Perhaps the shuttle picked this thing up in space? NASA cannot help the Avengers and they find that they have their hands full with coordinating mop-up operations with Agent Freeman. The Avengers leave the lab and the mystery object behind.
After the door closes, the capsule turns nearly transparent, revealing a sleeping red-haired woman within, who telepathically calls out the name Scott. A moment later, the power fades, the capsule grows opaque and silent once more and Jean Grey is once more hidden from the world.