Nina barely escapes the cruise ship with her life, and is taken to a Kometa Island research facility. Here, she encounters Lukas Hayes, a scientist who informs her about Kometa's plan to use satellites to heat and activate methane hydrate on the ocean floor. The result is bubbling which causes ships to lose their buoyancy. The weapon thus has the power to destroy naval vehicles from afar, sinking them to the bottom of the sea. Hayes' plan was to find a new energy source and alternative to fossil fuels, but his research was twisted into a form of warfare. The project is Salacia, the mysterious operation CIA and MI6 have heard rumors of. Nina realizes that she must stop the project, and takes on the second Kometa executive, Enrique Ortega. However, he is joined by Anna Williams (Nina's sister), hired along with the Tekken Force as bodyguards. After briefly engaging in combat with Anna, Nina continues on her mission and manages to kill Enrique. Lukas Hayes, however, is also killed as Lana Lei arrives and recovers a case which houses the electronics to operate Salacia's satellites. With Alan's help, Nina escapes the compound by helicopter, chasing Lana Lei back to the luxury cruise ship.
For a second time, Nina must fight her way through the Kometa boat, only this time against advanced cyborg soldiers, another of Lei's weapons projects. After recovering the keys to her quarters, Nina finds Salacia and engages with Lana. After her defeat, they are interrupted by Alan, who is revealed as Kometa executive Edgar Grant. Shooting Lana, he acknowledges that he is also a sweeper, there to destroy all evidence of his part in the atrocities. Before he can kill Nina, however, Lana shoots him dead, and escapes to a secret room. There, Nina witnesses her powering Salacia, targeting methane hydrate pockets all around the United States coastline. Nina finishes Lana off before she can continue with her insane plan, and makes her way to an escape pod as a self-destruct mode is activated on the boat. Her pod, however, explodes, and Nina lands on the ship's edge. As a rescue helicopter comes for her, she is knocked down by none other than Anna Williams. The two sisters face off as the ship nears destruction, and almost both fall to their deaths. However, the two grudgingly work together to escape and grab the helicopter rope line, with Nina having a flashback to the events prior to her father's death, in particular the moments following when the two sisters comforted one another. Anna drops Nina into the ocean after saying that they are now even. Nina watches on as rescue boats approach from behind her, the Kometa ship exploding and sinking, as Anna leaves on the helicopter.
The game's most remarkable feature is the ability to allow Nina to use her martial arts skills to break the bones of her enemies through use of carefully aimed attacks. These attacks do more damage to the enemy and show the player the damage being inflicted on the opponent's skeletal structure. Strangely, this does little to actually disable opponents, as they often continue to use limbs that have been literally shattered, as well as survive blows to the head that would cause the skull to practically explode, without even losing consciousness.
Once the game is completed, "Anna Mode" will be unlocked, offering the player the ability to play as Nina's younger sibling, Anna. Various outfits can be unlocked throughout the game, which include a bikini, cocktail dress, purple jumpsuit, black and silver stealth suit. Playing the game a second time causes LCD crates throughout the game to contain infinite supplies of certain weapons, such as infinite katana and infinite rail-gun. After completing the game twice, the wrestling costume as seen in the opening FMV is also unlocked. A third clear game file additionally unlocks "Tekken 2 Nina", which instead of an outfit is actually a different facial and bodily construction, exactly as she appears in the Tekken title, in low resolution.