In 1982, a Japanese woman prays at a crying statue of Mary. Apex Moth appears behind her, confirms that the statue's tears cured the woman's deafness, and gathers a vial for testing. The woman, whom Apex Moth identifies as a seer, says that miracles can't be understood like that. Apex Moth asks for the seer to look into his future and the seer says that she sees him surrounded by horrific monsters and causing unspeakable catastrophes — but, at the same time, being very much alone. She says she'll pray to avert this outcome. Apex Moth dismisses this as religious nonsense and leaves the church, only to find a strange man that gives him geographic coordinates. The man holds a match which burns with a weird light as he says that, if Moth goes to the coordinates when he's in the right frame of mind, it will be worth the trip.
In the present day, Black Hops — Ruby, Sawyer, USA GI, Patriot-R, Rigor Tortoise, Grendel, and new member Bazooki — finds the body of Ogopogo, a very powerful cryptid which Cryptiq killed. The task force determines they'll need backup if Cryptiq has become powerful enough to dispose of beings like Ogopogo. Then they're summoned to Japan for a new mission. Meanwhile, Bandit Okami meditates alongside his chupacabras while a couple of Yakuza gangsters swap rumors about his awesome capabilities. Hopkins shows up and shouts at Okami to get going; they leave (as do the chupacabras) while the Yakuza gangsters prostrate themselves. Hopkins also says that Cryptiq's new member is following behind her, and a woman passes by the gangsters while snakes crawl over them and make them flinch.
The Black Hops team travels to Tokyo Haneda Airport, where they meet up with Kimiko and Sylvia from the Kamen Corps; they are there at the request of Agent Hudson. It's noted that Kimiko has never worked with Black Hops before; and she's overcome with the cuteness of the animals and hugs them before Patriot-R proceeds to bite her. Sylvia explains the mission: the Kagemitsu technology which Black Hops (and Carly) previously recovered from Cryptiq has been stolen by Yakuza gangsters, who are meeting with Cryptiq to sell the technology back to them. Black Hops needs to attack the meeting, catch as many villains as possible, and make sure the bad guys don't escape with the tech. Because Hudson needs Carly herself elsewhere, the team will additionally be helped by Jessie McGrath, also known as the heroine Versema. Finally, Vicki Kaminski will be battling alongside them as well.
The team sneaks up to the meeting point and defeats all the Yakuza guards in a relatively stealthy manner, though Jessie is loud enough that Ruby criticizes her. The team then realizes that it's odd they haven't encountered any Cryptiq soldiers yet, at which point a wall in the building purportedly housing the meeting explodes. The heroes are knocked back as almost the entirety of Cryptiq — Okami, Hopkins, the Mimic, the Tatzelwurm, Stiletto, Keli's goblins, Okami's chupacabras, and a humanoid shark monster — attack.
Sawyer and Grendel go to secure the technology but Stiletto uses her powers to encase them, along with Vicki and Bazooki, in stone. Vicki, however, uses her own powers to break free. Vicki also frees Bazooki, who begins using explosives; meanwhile, Stiletto sends her army of snakes at her opponents. A wild melee ensues, during which time Bazooki uses his own power to turn to stone and lets USA GI knock him into the Tatzelwurm.
Vicki explains to the others how Stiletto's powers work and how they have to avoid looking her in the eye. Meanwhile, Kimiko flees the shark monster, now identified as Sawtooth. Kimiko tries to fight him but he's too strong, and when Versema tries to help, she's attacked by Hopkins. Versema manages to fend Hopkins off and trades enemies with Kimiko; she offers to give Sawtooth a head start fleeing if he just abandons the fight, then uses her super strength to throw him into the nearby sea. Meanwhile, Kimiko uses her water powers to sweep away Hopkins' goblins.
Sylvia duels Mimic, who is mimicking her powers and attacks, in the sky. Sylvia eventually realizes she should use her 'Victory Syphon' ability since Mimic can't copy that; she does so and drains his powers so he crashes to the ground. Meanwhile, Okami duels Patriot-R and Rigor-Tortoise, using his sword's power to block bullets in order to survive Rigor-Tortoise's powerful guns. However, when Patriot-R gets Rigor-Tortoise on a chain and begins using him as a melee weapon, Okami quickly loses.
While Cryptiq is steadily losing ground, Ruby realizes that Stiletto is going for the technology. She abandons her earlier insistence on being stealthy and has Bazooki attack with explosives. USA GI then attacks Stiletto's stunned form but finds that her skin is hollow; she shed it and escaped. Still, the rest of Cryptiq's forces on the scene have been defeated and captured (or, in the case of the critters like the goblins and chupacabras, killed), and Vicki is able to break Sawyer and Gremlin out from their stone shells. At that moment, though, Hudson sends Ruby a frantic message stating 'Code Ashita.' Ruby has no idea what that means.
Hours before the battle, Hudson meets with Kamina, Jackknife, and Pitchfork in his floating base. Noting that most of Black Hops (and also Vicky, who is usually in Spec Hops) are busy in Japan, he brings in Carly and Misha to reinforce what's left of Spec Hops before beginning to discuss their mission. He says that Apex Moth not only needs Kagemitsu's technology but he also needs to reverse engineer some of it, and so he stole the brain of the deceased Dr. Arigaki. The Spec Hops team and their helpers need to stop him from using the brain to do whatever he'll do with it. Carly, who bears a deep grudge against Arigaki for the death of her father, is eager to take the mission on.
Father Retter enters and says they've tracked Moth to an eldritch location called Longharbor. Kamina doesn't think Longharbor is anything more than a spooky legend, but Retter says it does exist, though it isn't always present in the real world. Since it's present now, though, they need to move fast and stop Moth from exploiting it. They believe Moth is in the lighthouse and divide the team into two: Pitchfork, Jackknife, and the Lovacova sisters will sneak in through the marsh, while Carly and Retter will openly approach by shore and hopefully divert Moth's attention.
The marsh team advances with Pitchfork taking the lead on account of his survival expertise. Kamina is derisive of Misha's abilities, and even when bizarre eldritch tentacles attack, the Lovacovas bicker while fending them off. Meanwhile, Carly and Retter are attacked by an eldritch crab. They fight it and hold it off until Hudson's advance scout, Regina "Rags" Ragowski, shows up and helps them defeat it. Ragowski complains that she was more or less drafted into this job and abandoned on the island, but Retter says they need to keep moving. He also observes how angry Carly is and he urges her to let go of her wrath. Carly insists she just wants closure, not vengeance, and asks Retter to have faith in her.
The marsh team continues with Kamina killing everything that attacks either her or Misha, and when Misha complains that she's not helpless, Kamina says that Misha's marksmanship is poor and she can only fight by just blasting everything in sight, whereas Kamina herself can fight more surgically. The argument is interrupted by a bomb attack which Misha manages to incinerate before it explodes. The attack came from Vulkan Faust, an enemy Misha is sure she previously killed. Faust taunts that he broke out of Hell to kill her and would have done so before but Moth kept him busy harvesting cryptids. He then attacks with massive firepower. Pitchfork and Jackknife are able to drive him back, but he doesn't fall, and he keeps fighting along with other monsters.
The shore team hears the fighting. Carly realizes that there's no point in serving as a 'distraction' anymore if the bad guys already know of the marsh team (which they clearly do, given the battle), so she flies Rags and Retter to the lighthouse. They encounter Moth, who attacks them with a giant robot controlled by Arigaki's brain. The brain is able to survive without its body because of something in Longharbor's eldritch nature, and as long as the brain itself is alive, it can power the robot. Retter, however, fires a powerful shell, and when Carly zaps it with her powers she's able to detonate it and disable the robot.
Carly says she wanted to confront Arigaki as a man but now sees him as a monster. She says she's both satisfied with his fate and also pities him, noting how he's trapped in the monstrous robot body. She leaves to help Rags fight Moth while Retter uses more munitions to blow up the rest of the robot. The shore team then all confront Moth together, only for the mysterious man he met back in 1982 to appear. He has an obsidian match in his hand and Retter identifies the figure as the demon Blackfire. Retter tells Rags that bullets won't stop Blackfire while Blackfire teases Moth about how he will never master Longharbor's powers without help. He advises the others to run while he speaks with Moth in private.
Retter orders a retreat and tentacles swallow the lighthouse as the shore team flees. Carly is able to fly, and Rags uses her magical outfit to both fly and also give Retter flight powers too. At that moment, they also get the 'Code Ashita' message, as does the marsh team which too is forced to retreat. The marsh team makes it to a raft provided by an old man, but the man vanishes when they look again.
Later, at Area 51, it's revealed that Hudson called in the Code Ashita upon seeing the tentacles swallowing the lighthouse. He says that the team cannot return to Longharbor while the tentacles remain. One of Hudson's superiors says Moth may have been killed in the tentacle attack, but Hudson doubts it, and indeed Moth turns up back at his base with Stiletto, the Tatzelwurm, and the remnants of Arigaki's robot body drilling into a skull.
A flashback shows Hudson sending the Code Ashita message when tentacles attack his floating base. Code Ashita turns out to summon Tomorrow Girl, who arrives in the nick of time and destroys the tentacles attacking the boat. In an epilogue, Ruby reports that the captured Cryptiq warriors were imprisoned, and Gracey notes that a new oversight committee will now prohibit teams like Black Hops and Spec Hops from getting outside help. He says he and Vicki are working to develop ways to get stronger so they can overcome this new handicap; behind him, a robotic bunny mask sits on a shelf.
- Attack Pattern Alpha: 'Code Ashita' turns out to be an attack in which Tomorrow Girl is summoned to help fight.
- Crossover: Characters from Antarctic Press comics, including Versema, Rags, and Tomorrow Girl, show up in this comic.
- Mirror Match: Sylvia winds up in one of these against Mimic. She wins when she uses her Victory Syphon power, since Mimic can't copy that one.
- Opponent Switch: Kimiko and Versema do this. Kimiko isn't strong enough to handle the powerful Sawtooth while Versema's tough but slow attacks aren't effective against the mob of goblins that Hopkins can wield. They thus swap, allowing Versema to use her heavy strength against Sawtooth while Kimiko simply sweeps away the goblins with her water attacks.
- Parrying Bullets: Okami can essentially do this due to his sword's ability to repulse incoming projectiles.
