Another feature returning from F-Zero GX to F-Zero NX is the inclusion of a story mode. This game differenciates itself from GX's Story Mode by including a cinematic campaign for each character, wherehas GX only focused on Captain Falcon. The player must complete 6 different scenarios throughout each story, and some characters will occasionally cross over into each other's stories, in a vein similar to F-Zero GP Legend. The cutscenes are presented in a semi-still motion (save for each character's ending, where they are presented in full motion) with anime art provided by Studio Gonzo, who also worked on the cutscenes in Street Fighter IV. Most, if not all of the stories are centered around Blood Falcon's war on the galaxy. A true ending to the game, which brings together the most important characters and resolves the plot, is unlockable by completing the stories of Captain Falcon, Dr. Stewart, Mighty Gazelle, Beastman, Super Arrow, James McCloud, Roger Buster, Jack Levin, Leon, Phoenix, Megan, Rick Wheeler, and Virgil Hogan. A summary of each character's story is displayed below.
Captain Falcon: Old Foes[]
Captain Falcon's story begins with him in his iconic Blue Falcon, trekking the dusty plains of Red Canyon. He is on the phone with Jody Summer, who is apparently trying to convince him to do a certain job for free. Falcon denies her request repeatedly, stating that he does not want to be "too heavily influenced by the Federation". He then realizes that he has absent-mindedly wandered into Samurai Goroh's home turf. Upon noticing a few of his rival's goons gathering on a cliff, he hangs up with Jody and slows down his vehicle. Upon coming face-to-face with the samurai, he is accused of seemingly kidnapping his son, Dai Goroh. Falcon is confused by this revelation and denies any involvement with the boy's disappearance. This angers Samurai Goroh, who then challenges Falcon to a race. Should Falcon lose, he must hand over Dai Goroh and never come near his family again. Falcon does not bet on anything should he win, still not knowing about what happened to Dai.
Mission 1: Beat Samurai Goroh to the goal!
Falcon is able to defeat Goroh and races out of the samurai's base camp. He contacts Jody again and tells her about Dai Goroh's disappearance. Jody hears about Goroh accusing Falcon, and gets the idea that Blood Falcon may be involved. Falcon agrees with her, and complies to work with her on this case. Jody tells him to meet her at the Outer Space colony the next morning.
Deploying the Blue Falcon out of the autopiloted Falcon Flyer, Captain Falcon sees a group of 19 vehicles riding across the colony. He recognizes them as Dark Million foot soldiers, and realizes they are headed straight for Jody's dropship. Falcon intercepts the soldiers, and they notice him and retaliate.
Mission 2: Destroy the Dark Million foot soldiers before they get to Jody's dropship!
After destroying the enemy machines, Captain Falcon shrugs off the attempt to foil their plan until he sees another machine zoom past. Suddenly, the White Cat races straight toward the vehicle and crushes it with a Spin Attack. Jody contacts Falcon and jokingly states how he is "sexist" for thinking she "can't take on these mooks". Falcon and Jody meet in person aboard the dropship, and Jody briefs Falcon on the Blood Falcon's uprising and the recent reappearance of Deathborn. Falcon is shocked by the revelation that Deathborn is still alive, and demands to find where he is. Fortunately, Jody receives an anonymous tip that the former tyrant is somewhere in the Infinite Wastes. They both are suspicious of the sudden hint, and Falcon reluctantly agrees to carry an emergency backup signal in case they find themselves in trouble.
Hiding in the junkpiles while staking out Blood Falcon, seemingly in contact with someone, Jody warns that this scenario is "most likely a trap". Trailing Blood Falcon after he gets back in the Blood Hawk and races away, Falcon notices they are headed straight into Jody's aforementioned trap, and tells her to split up with him, giving her coordinates to meet again at. Still trailing behind Blood Falcon, the bounty hunter seemingly trips something that slows down his machine greatly. His clone turns his machine around and mocks his template for falling so easily into his trap. Blood Falcon rams into his template's machine and knocks him down into the garbage line below. The machinery is old and unstable, and Captain Falcon finds his machine weighing down heavily on it.
Mission 3: Your machine has no boost and is very slow! Get to the end of this garbage line that is falling apart!
Barely escaping, Falcon gets back to the rendezevous point, where Jody seems to have survived some kind of predicament as well. Jody warns Falcon that Deathborn is, in fact, on the planet, and that he is seemingly "hungry for revenge".
Falcon and Jody soon find themselves inside the ruins of a 23rd-century Galactic Federation ship. Jody, ready for anything, pulls out her signal, only to find it is damaged from her encounter with Deathborn. Falcon finds his signal to be similarly fried. The duo discovers the Dark Schneider racing across a hazard-laden track, and the two quickly hop in their machines to catch up with the Dark Emperor.
Mission 4: Don't let Deathborn out of your reach!
The duo is able to make it to the end of Deathborn's track, to which Deathborn sarcastically congratulates them on. They both question Deathborn as to how he is alive and what he plans on doing now. Deathborn explains to them his method of ressurecting himself and tells them of his ulterior motive; to "free" mortals from suffering. Deathborn then states his plan to challenge them to a race in Silence. Before Falcon and Jody can apprehend him, Deathborn warps away with the Dark Schneider.
Deathborn arrives on Silence, where Falcon and Jody are waiting for him. They both tell him that it's the "end of the line" for him and that the both of them don't plan on letting him walk away. Deathborn laughs off this threat and tells them that he "will be walking away, but he won't be walking away". Falcon and Jody are confused by this rhetoric, until Deathborn creates 28 other clones of himself, and they all tell the duo in unison that only one of them is real. Then, the race begins...
Mission 5: Destroy the real Deathborn's machine before the end of the race! You can tell who it is when all the others vanish!
The Dark Schneider spirals out of control, and crashes into a guard rail. Falcon and Jody celebrate the tyrant's defeat, only to realize he is still alive, and Falcon is shot with a dark energy blast, knocking him out and leaving him in fatal condition. Deathborn cackles over his "ironic victory" and vanishes yet again. Jody uses a new communicator and calls in her dropship, desperate to get Falcon to the hospital.
While unconscious, Falcon sees visions of the Dark Million members defeating their rivals. In his subconscious, Deathborn reappears alongside Black Shadow and Blood Falcon. Captain Falcon is caught off guard by this, and suddenly, a new racetrack appears, with his rivals challenging him to a battle to the death.
Mission 6: Falcon's rogues gallery is here! Win the decisive battle against them!
Captain Falcon is able to come back to consciousness after defeating his illusory enemies. He realizes Jody's attempt to save him, and can't thank her enough. Jody doesn't have time for praise, as she warns Falcon that the entire Dark Million has been pinpointed to a single planet. Falcon joins up with the Mobile Task Force and sets out on the journey to defeat Deathborn once and for all.
Dr. Stewart: Father Knows Best[]
Dr. Stewart's story takes place on the 20th anniversary of his beloved father's demise. The doctor pays his respects to the racing legend Kevin Stewart by leaving a half-empty bottle of what is apparently "his favorite beverage". He thanks him for being his father, and promises he will not let his legacy die out. Riding the Golden Fox through Mute City, Stewart notices some kind of F-Zero machine approaching him. He immediately recognizes it a the Wild Goose, which none other than the infamous Pico pilots. Fearing for his safety, Stewart boosts ahead.
Mission 1: Don't let Pico catch up with you!
Merging into a freeway, Stewart judges that he has lost the hitman and calms down.