Ophelia is just finishing her two years of ninja training with Nunchuk, T'Jbang, and Snake-Eyes, the Silent Master. Ophelia is the last ninja to be trained by the Arashikage Clan. She has passed all the tests but the final one which is left up to fate.
Scarlett and Snake-Eyes are engaged and nearly a year from there wedding date.
Elsewhere, Sean Collins and his dad, Wade Collins, are having a conversation about their military service. They talk about the letter Sean wrote to Snake-Eyes. And how much Wade has been helped by Snake-Eyes. Wade, now considerably beat down by the recent death of his wife, is getting the news that Sean is joining an elite unit of the military and being sent on a mission, all classified stuff.
A year passes.
Scarlett is having doubts about the wedding. Stalker reassures her that Snake-Eyes will marry her. Snake-Eyes has continued to train Opheila even though her final test hasn't happened, yet
Hammer team is assembled with Conrad Hauser (Duke) and Special Agent Provost (Chuckles) leading this non-GI Joe team. Their mission is to capture Firefly. Chuckles has set up an arms deal at a facility in Ohio with Firefly. And now Firefly will be walking into a trap set by Hammer team.
Snake-Eyes and Opheila have this information about Firefly's appearance in Ohio, which is through an independent source of the Hammer team. This mission is to be Opheila's final test; if she passes she becomes a ninja, and full member of the Arashikage Clan.
As soon as Firefly detects the trap he starts blowing up cars and building. He kills all of the Hammer team except Sean Collins. Snake-Eyes and Opheila enter into the middle of the fight, Duke and Chuckles recognize them. As Firefly is about make his escape, Opheila attacks him; Firefly gets the upper hand in the fight and shots Opheila. Snake-Eyes can not save her, and Firefly escapes.
Snake-Eyes misses the wedding, Scarlett breaks up with him, Opheila is buried, and Sean Collins joins Snake-Eyes out in the High Sierras retreat. He is to become Kamakura the last ninja to be trained by the Arashikage Clan
Sean Collins is being trained to become the last Arashikage ninja Clan member. Nunchuk is teaching him the forms and weapons of the Clan, T'JBang is guiding him on the mental and spiritual, and The Silent Master, Snake-Eyes, is continuously testing him.
About a year passes; Kamakura is now ready for his final trail. That mission will be to take out Firefly. Jinx, Budo, Snake-Eyes and Kamakura are in Tokyo. Jinx has gathered information on a mysteries figure called the Nowhere Man, and has learned of a meeting between the Nowhere Man and Firefly. The group makes a plan to attack Firefly at this meeting.
Kamakura is looking for revenge for the loss of his Hammer team to Firefly. Snake-Eyes is looking for revenge for the death of Opheila.
At the meeting, none other then Storm Shadow shows up instead of the Nowhere Man. Storm Shadow is Snake-Eyes' long time friend and rival. Immediately Snake-Eyes jumps in to action at the sight of Storm Shadow. Kamakura quickly follows as Jinx and Budo remain in sniper positions as support.
After Snake-Eyes initial attack, Kamakura enters the fight and is cut by Storm Shadow. Snake-Eyes moves to help Kamakura. This gives Storm Shadow the opportunity to finally end the conflict between the two sword brothers.
As Storm Shadow is about to strike down Snake-Eyes, who is holding an injured Kamakura, Jinx saves them with a well placed sniper shot to Storm Shadow's sword. Snake-Eyes then goes on the offensive and the fight spills out into the hallway. Jinx and Budo move into extract Kamakura. Firefly, who was there to meet Storm Shadow, moves in to kill Kamakura, and a stand off between him and the team of Jinx and Budo, takes place. Firefly calls for extraction.
The Nowhere Man has sent Firefly to meet with Storm Shadow.
The fight between Storm Shadow and Snake-Eyes has moved to the roof where Firefly's military extraction helicopter is coming in from. The helicopter has orders from Firefly to shot Snake-Eyes and Storm Shadow. Snake-Eyes dives and covers Storm Shadow to save him from the bullets. Snake-Eyes throws his sword into the helicopters window. As he is doing this Storm Shadow stabs him in the back with a small knife. Storm Shadow is about to cut Snake-Eyes throat when the helicopter runs into a sign that falls on the both of them.
Firefly is waiting for extraction and holding Kamakura as protection. Kamakura frees himself, and Firefly jumps to the waiting helicopter, which then proceeds to shot Jinx and Budo.
Storm Shadow recovers quickly from the sign falling, and is then shot by a tranquilizer dart from Firefly. The meeting was a set up to capture Storm Shadow. He is then taken up into the helicopter. As Snake-Eyes is being brought up to the helicopter, two mysterious figures come out of nowhere to save him.
Firefly receives orders from Nowhere Man to leave with Storm Shadow.
The next day the two mysterious people are revealed to be Chuckles and Duke. And that Storm Shadow was working with Duke to bring down the Nowhere Man. The Nowhere Man is Kamakura's old Hammer team leader Mikhail Derenko. Kamakura doesn't believe it because he was supposed to have died three years earlier at the same time as Opheila died.
Duke and Snake-Eyes have a private meeting. Where Duke shows some video of Scarlett and threatens Snake-Eyes with bring her in to help him out with the Nowhere Man, if he doesn't go along. Of course, Snake-Eyes is in.
Kamakura and Budo have a moment where Kamakura is put in check about his sloppiness and how the need for revenge is causing it. Kamakura calls his father, Wade, to help clear his head. As Wade Collins hangs up his phone Mikhail Derenko and Firefly, with the tranquillized Storm Shadow, welcome him back to the Crimson Guard.
Firefly, Wade Collins, and the Nowhere Man (former Hammer Team leader Mikhail Derenko) are in a Tokyo night club, a Cobra front, trying to break into a secret vault. Wade Collins, who has the face of a "Fred" series Crimson Guardsman, can access the vault using his facial recognition. Wade has agreed to accompany them to gain some information on Firefly to help his son, Sean Collins. Storm Shadow, who has just escaped from Firefly, is inside the building and able to send a signal that Duke receives.
Snake-Eyes and Kamakura are going over the events in which Firefly killed Opheila, and the Hammer team. Kamakura has come to the realization that Snake-Eyes loved Opheila like a sister. (Snake-Eyes' twin sister had been killed in a car accident with the rest of his family on the day he was returning from Vietnam) And that nobody else has realized that. Opheila, Scarlett, and Snake-Eyes' sister all have a similar look to each other. Kamakura apologizes and pledges himself to fighting the Arashikage Clan way. And Snake-Eyes and Kamakura go off to fight Firefly and Derenko, aka the Nowhere Man.
Duke reveals that he and Chuckles had given Snake-Eyes the intell on the Hammer raid. Which was why he and Opheila were there the night Hammer team was killed. Duke had suspected a traitor among the Hammer team, actually thinking is was Sean Collins. He set up the whole deal to trap Firefly and to reveal the true traitor. The traitor turned out to be the team leader Mikhail Derenko. Duke also reveals that he has been working with Storm Shadow to catch the Nowhere Man and knows were Firefly is holding the captured Storm Shadow.
Duke, Chuckles, Snake-Eyes, and Kamakura make a raid on the night club that holds the Cobra vault with intention of capturing Firefly and rescuing Storm Shadow. Kamakura finds and begins to fight Derenko. Derenko is winning and Wade Collins steps to help his son, in the ensuing fight between the three, Kamakura accidentally stabs his father, Wade with his sword. As Wade lies dieing in Kamakura arms and Derenko makes his escape, they express their love for each other. Kamakura then takes off after Derenko to avenge his father's death.
Snake-Eyes meets up with Storm Shadow and they form an uneasy truce as they are both attacked by Firefly's men.
Duke and Chuckles along with the rest of the team escape from the building as Firefly's makes a warning that the building will blow up in two minutes.
Kamakura who catches up to Derenko slings throwing stars at him, one catching Derenko in the eye. A car arrives to wisk Derenko away. In the car, a women with black hair attends to the wounded Derenko, he informs her that the vault they were trying to access was a failure, that the E.M. (Electro Magnetic) bomb is still a secret and their long term operations are not affected. The bomb Firefly informed the team about was a fake one.
As they load Wade Collins' dead body into the ambulance. Storm Shadow talks to Snake-Eyes and Kamakura explaining that the Cobra brainwashing program that he has been subjected to for years has not only programmed him to serve Cobra, but that it plays on his weakness for his old friend Snake-Eyes. And that it forces him to attack Snake-Eyes, and currently his adrenaline is blocking the brainwashing. He walks away before the urge to fight Snake-Eyes takes over. He praises Kamakura for following his families, the Arashikage Clan, way and promises his friends that he will fight his brainwashing on his own.
Three weeks later Jinx, Nunchuk, T'J Bang, Snake-Eyes, Duke and Chuckles are at a small ceremony to honor Sean Collins for becoming a full member, actually an apprentice master, of the Arashikage Clan, He chooses his new name, Kamakura and reveals his new arm tattoo, the same Arashikage Clan symbol worn by Snake-Eyes, Storm Shadow and the rest clan
In the South China Sea, a fight is happening, people are betting on a young woman who has beaten all comers. One last fighter steps up to fight her. That fighter is Storm Shadow, and in the audience is Billy (Cobra Commander's son and Storm Shadow's 1st apprentice) placing bets that Storm Shadow will win the fight. Storm Shadow fights the young woman and wins. In the middle of the fight, Storm Shadow sees a devil in the crowd, a reflection of the brainwashing that he has been through at the hands of Cobra Commander's brainwave scanner. As Billy and Storm Shadow are counting their winnings outside the area, the young woman approaches and Storm Shadow introduces Billy to Junko Akita. A crowd from the fight sees them together and chases after them as they make there escape, again Storm Shadow sees a devil in the crowd.
Tokyo, Japan: Junko, Storm Shadow and Billy are sitting at table talking: Junko Akita's History: Her father Haro Akita worked as a sensei and personal security trainer, and was killed by the Japanese mafia, Yakuza. She was fifteen when it happened. After the funeral, the man who killer her father, Ryuji Hyata, came to her house and killed her mother. She witnessed her mother dying, and at that moment vowed her revenge against her parent's killer.
She began to train as a geisha in order to get close to the killer. She spent years training as geisha during the day and at night keeping herself in fighting form. At the age of twenty, she got her chance. As she was in a room alone with Hyata and as he was making an advance on her, she stabbed him right in the heart, killing him. Her patience had paid off.
As she was fleeing from the scene, she literally crossed Storm Shadow.s path. Storm Shadow called it destiny.
On the streets of Tokyo, Storm Shadow was riding his motorcycle feeling empty and shallow about six months after the events of a CIA black ops operation. (The 1st Master & Apprentice series) As he turned a corner, Junko escaping from Yakuza crossed his path. His first inclination was to keep going, but it was destiny not to continue on his current path. As Junko started fighting the group that was chasing her, Storm Shadow jumped in to assist in dispatching the entire group of Yazuka. He took her home and attended to her wounds. Junko had completed her task and was ready to move onto a new life. She became Storm Shadow.s apprentice and lover. And he was able to keep her hid from Cobra Commander for years.
Standing on a balcony with his uniform burning in a pit, Storm Shadow is still bothered by the brainwashing, which appears in the form of a devil face, even though he has been able to shake off most of it. The brainwashing still has its effects. He is afraid that this current clarity of mind will not last. But Junko assures him that she and Billy are there to help him prevent any relapse. And that he can move on with his life.
Just as Billy finishes a speech about starting a new life, Cobra Commander appears with a group of Night Creepers.
Cobra Commander, with the support of the Night Creepers, surprise Storm Shadow, Billy, and Junko Akita (Storm Shadow.s apprentice and lover) at his home in Hong Kong. Cobra Commander leaves the scene as the battle rages between Storm Shadow and the Night Creepers. After an extended fight, Billy and Storm Shadow make it to the elevator. As Junko is arriving at the elevator a Night Creeper sets off an explosion that separates them. The explosion pretty much destroys the floor of the building and the elevator Billy and Storm Shadow are in crashes to the lower levels.
Slice and Dice make there appearance at the scene to collect the injured Junko.
As Storm Shadow awakens in the hospital a day later, he discovers that Junko was not recovered from the explosion. The devils of his dreams have returned these devils are really just an after effect of the brainwave scanner treatments. These treatments, which he has received for several years and just recently broke free of, still haunt him. His latest dream is about how much he has destroyed his family, Snake-Eyes and now Junko.
A couple of days later Storm Shadow and Billy now joined by Jinx and Budo inspect the destroyed home. Budo pledges his help, and Billy discovers a message scratched in the dust from Junko. It is an Arashikage Clan symbol.
In Tibet, at the main sanctum of the Red Ninja Clan, T.JBang, the now surrogate leader of the Clan since Snake-Eyes took control, has an exercise training opponent set up for him by a member of the Clan.s staff. T.JBang begins the exercise blindfolded, his skillful opponent, reveals himself to be Sei Tin. Sei Tin is the deposed, by Snake-Eyes, former leader of the Red Ninja Clan. T.JBang is cut but not killed and taken prisoner. Slice and Dice arrive with the captured Junko. And it is revealed that Sei Tin, who helped by Cobra Commander got a titanium backbone, is now working for Cobra.
Storm Shadow, Budo, Jinx, and Billy begin the preparation and search for Junko.
After months of searching for the missing Junko Akita, Storm Shadow, Jinx, Billy, and Budo have finally found the lead they have been hoping for during there most recent Cobra raid. That destination is the Tibetan mountain retreat of the Red Ninja Clan. The Clan.s former leader Sei Tin, who was displaced by Snake-Eyes, has taken back his leadership of the Clan. (see issue #27 of the main series, and M & A 2 #2 for these events). Storm Shadow and Jinx are unaware that Sei Tin, has removed Snake-Eyes. surrogate ruler T.JBang.
At the retreat, Sei Tin, Slice & Dice are putting Junko through all kinds of mental and physically torture, as well as isolation, all in order to breakdown her will. They are using old fashion brainwashing methods (with some natural medications, but no technology) to turn her against Storm Shadow. Making her think that all the pain they have caused her was brought onto her by Storm Shadow himself. The final moment that turns her love for Storm Shadow into true hatred for him is when, after a long period of isolation, she is just let out of her cell. She then makes her way to the exit of the Clan.s retreat, where she is confronted by Storm Shadow himself. Just as Junko is amazed to see her lover, who has come to rescue her, she is sliced by his sword, bringing her even more pain, and almost to the brink of death. This ultimate betrayal is a set up to turn her against Storm Shadow. The 'Storm Shadow' that cuts Junko is actually Dice in disguise.
The real Storm Shadow attempts to contact Snake-Eyes, and mounts his rescue mission with the help of his cousin Jinx, his former apprentice Billy, and Jinx.s boyfriend Budo. Storm Shadow and Jinx are dropped off by the chopper flown by Budo with Billy as co pilot. Budo sends out a message to the Joes that they are in Tibet on this rescue mission. Storm Shadow and Jinx invade the retreat on there own.
As Storm Shadow and Jinx enter the retreat they come to a room filled with dead Red Ninjas and a man chained to the wall. Jinx investigates the man, discovering that it is actually Sei Tin with a repaired spine.
Sei Tin surprise attacks Jinx. Jinx is now held between Sei Tin and Storm Shadow. Storm Shadow hears Junko calling out to him. Jinx makes a move to free herself, and begins to fight Sei Tin, as Storm Shadow takes off after Junko.
As he climbs toward the voice of Junko, he runs into a mysterious person in a red cape, with a green death mask on. Storm Shadow is forced to fight this mysterious masked opponent. This opponent gets the upper hand by talking to Storm Shadow about Junko. Storm Shadow is stabbed by the masked opponent just as she reveals herself to be Junko. He is horrified.
Jinx is then knocked out by Sei Tin. Billy and Budo are ambushed inside their chopper, after it lands, by Slice and Dice. All seems lost.
At the GI Joe operations center in D.C., Kamakura receives Budo's message.
And now it is going to be Snake-Eyes and Kamakura to the rescue.
Inside the Red Ninja Clan's Tibetan retreat, Storm Shadow has just discovered his lover and apprentice, Junko Akita has been brainwashed by Sei Tin, at Cobra Commander's orders, against him.
Jinx, T'J Bang and Storm Shadow are all captured by the numerous Red Ninja Clan members.
Outside the retreat, Billy and Budo are fighting against Slice & Dice inside the rescue chopper. As the chopper is crashing Budo throws the injured Billy to safety and jumps clear of the wreckage. The next morning Budo and Billy awaken to Snake-Eyes and Kamakura.
Inside a ring of fire, Storm Shadow awakens to discover that Junko has been brainwashed as punishment for Storm Shadow's escaping from Cobra Commander. Sei Tin is punishing Storm Shadow by punishing those closest to him. Jinx & T'J Bang are to be sacrificed. Junko steps up to face Storm Shadow in one on one sword fight.
Snake-Eyes, Kamakura, Billy and Budo have begun there attack into the retreat, fighting a furious battle to reach Storm Shadow. Many Red Ninja Clan members are killed. As Jinx and T'J Bang are being taken away by Sei Tin, Snake-Eyes and his team meet them. Slice and Dice, who also survived the helicopter crash, join in the fight.
A large group battle begins: Jinx frees herself and helps get T'J Bang clear of the fight. Individual battles breakout, Budo protects Jinx from Dice, Sei Tin fights Snake-Eyes, and Kamakura takes on Slice. Slice and Dice are both defeated.
Snake-Eyes and Sei Tin are again fighting (see main series issue #26 for their first fight) for control of the Red Ninja Clan. As they come to a stalemate. Three loyal to Snake-Eyes Red Ninjas step in with bows and arrows and kill Sei Tin. Snake-Eyes is now recognized as the Clan's final leader.
During this large group fight, Storm Shadow and Junko Akita have been fighting there own private fight with swords and words. Storm Shadow continually tires to break Junko's brainwashing. Junko gets the better of Storm Shadow and she has him on the edge of cliff about to deal a killing blow. Billy arrives screaming at Junko �you're about to murder the man you love, lay down your sword�. This gets through the brainwashing, and realizing that she can't live with the brainwashing. Junko throws herself off the cliff and falls into an underground river.
Five days later, the team plus six of the loyal Red Ninja's bury the dead. The leadership has returned to Snake-Eyes, who then in turn hands it to Storm Shadow. Storm Shadow is reborn as the Phoenix Master of the Arashikage Clan. And the six remaining ninjas will form the core of the new Arashikage Clan.
As a final moment, Billy walks of into the mountains to finally find a way to be on his own. Storm Shadow reveals that he could not find Junko's body, and that he is finally clear of the Cobra brainwashing. It ends with a prayer to God by Storm Shadow to someday return his love to him.
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