Two years after the previous events,
Bayman's military patrol is ambushed and cut down by a hooded figure of superhuman speed which then dissolves into thin air. Seeking revenge, Bayman meets
Helena Douglas aboard her cruise ship,
Freedom Survivor, as he is suspecting DOATEC's involvement, which Helena denies, suggesting it might be rather the work of
Victor Donovan's breakaway faction. She is also approached by
Kasumi, who is looking for information regarding
Alpha-152 after the latter's sudden disappearance during the TriTower's destruction. Helena promises her help and arranges a meeting between
Hayate and Kasumi, who insists that the pursuit of Alpha is only her fight, rejecting Hayate's offer to aid her. Kasumi then sets out to find more clues about Alpha's whereabouts, going round-the-world while being herself pursued by
Ayane. She is also hunted by Bayman, who suspects Kasumi of being the attacker and desires to take her down himself. Helena informs Hayate that she will stop Project Alpha. Meanwhile, at DOATEC's oil platform, one of the platform's worker named
Rig, is paid a visit by
Christie, who claims to be a woman from his past coming to "test" him, and who is still working for Donovan. Soon, the platform mysteriously comes under helicopter attack, but Rig along with
Bass Armstrong, who's also employed there, succeed in putting down the fire. Donovan, his face hidden behind a porcelain mask, is seen plotting the final stage of his Project Alpha: Phase Four. Donovan orders
Lisa Hamilton, who is still working with him on her research, to bring head of DOATEC Japan,
Miyako, who too is part of their new organization, "MIST", to a secret laboratory located under the rig. Various characters are shown entering the fifth Dead or Alive tournament, which also takes place at the platform. Each does it usually for their own reasons, often to either see once more or to defeat some other character. They join after being approached by
Zack, who is shown finding, fighting and recruiting them around the world. After
Tina Armstrong decides to return to fighting, her father Bass enters it as well, adopting a ring name of Mr. Strong; eventually, they reunite as a team. While stalking
Jann Lee,
Leifang eventually confronts him before the tournament on a train and there is sexual tension between them when the train is thrown off its track and crashes.
Hitomi, who still hopes to see
Ein (Hayate), advances to the quarterfinals, defeating Spanish newcomer,
Mila, and then
Eliot. During a break, Hitomi meets Hayate, who wishes her good luck. Jann Lee, who had won constructive matches against Leifang and Mr. Strong, defeats Hitomi, emerging as the winner of the tournament, but not attending the championship award ceremony out of a personal grudge for Rig, whom he lost to in an earlier fight. In Japan,
Ryu Hayabusa is approached by Hayate and joins him and Ayane. Aboard Freedom Survivor, it is revealed to the Mugen Tenshin ninjas that Helena ultimately destroyed the Tri-Tower to get revenge on Donovan for both the death of her parents during power struggles within the organization and for turning DOATEC into a corrupted, immoral and in-human organization. Helena informs them that the Phase Four will see a mass production of Kasumi clones to sell them to top militaries in the world. Feeling that something is wrong with Kasumi, Hayate orders Ayane to follow her and discover her real intentions. Frustrated with her failure to track down Alpha, Kasumi returns to Helena, demanding to be told the truth, and Helena directs her to the platform. There, Hayate wins the right to follow her from Bayman. Kasumi discovers the lab, with Alpha-152 in it, and appears to destroy her clone. However, she is then attacked and mortally wounded by Hayate and Ayane, and dies in Ryu's arms. This Kasumi is revealed to be merely a clone herself, but Ryu regrets her death anyway. Ryu destroys attacking helicopters (of the kind that attacked the rig earlier), while Hayate is captured in the lab by Rig, who turns out to be working with Donovan. Ryu sends a falcon with a message for the real Kasumi, who has been sheltering with
Muramasa all that time; she immediately joins them up at the platform. In the lab, they defeat Rig, who escapes after saying it was a plan to lure them there. Lisa, dismayed to find out that Project Epsilon has been reactivated, frees Hayate. Alpha-152 then appears, taking forms of not only Kasumi but also of Hayate and Ryu, but Hayate, Ayane, Ryu and ultimately Kasumi, succeed in destroying her along with the lab. In the epilogue, Kasumi peacefully parts her ways with Hayate and Ayane, as Ryu and Helena watch by, and promises to herself to bring down Donovan for good. In the post-end credits, a conversation between Rig and Donovan (the former revealed to be Donovan's son) is heard. With Rig's success in gathering samples from the fighters, Project Alpha can now move on to Phase Four. ==Development==