Star Fox: The Final Assualt is a fan game that replaces Star Fox Command as the final chapter in the Star Fox Saga, for Wii U.
15 years have passed since the Lylat Wars, and Corneria is celebrating the anniversary of Andross´ defeat. The Star Fox Team is celebrating there too, with Miyu Lynx and Fay Spaniel as their new members. Peppy has replaced General Pepper, Slippy has a relationship with Amanda, and Fox is planning to propose to Krystal soon. Amidst the celebration, strange ships that resemble Venomian aircraft with bizarre symbols attack. Andrew Oikonny has returned, and he sends to an ultimatum to Corneria. General Peppy refuses, and Oikonny declares war, mentioning that he works for a new master, someone stronger than anyone in the galaxy. Puzzled and surprised, the Star Fox team repels a small battalion of Oikonny´s invaders before he escapes.
Due to Slippy getting himself into trouble with Venomian battleships, the Star Fox team follows him and the battleships to Meteor. Fay, being a talented communications expert, manages to notice that the battleships are coming from Sargasso. Star Fox arrives there, and finds out that Oikonny´s forces are stealing minerals from the colony ruins. Fox leads his men there, only to be met by Star Wolf, with Katt Monroe as their new fourth member, much to Falco´s dismay. After bickering and a fighting for a moment, Wolf admits that they are also looking for clues on the invaders. Fox is distrustful of his old adversary, but still lets him go and keeps on looking. They find Peppy´s daughter, Lucy Hare, who had been captured there during the Aparoid Blitz. She, along with many other prisoners, was forced to mine for the precious minerals that Oikonny and his master were going to use for superweapons. When Fox asks for whereabouts on her captors, Lucy mentions that Wolf asked the same thing from her, and she told him that the captors were going to test the weapons on Papetoon.
Meanwhile, Wolf and his team manage to fight off a few of the superweapons, and eventually discover the plans to the weapons. Suddenly, Panther takes the plans for himself, revealing that he is going to take them to Oikonny. Wolf is devastated, but Panther convinces him that he has been "too soft" lately, and that he has forgotten their principles of trying to be nothing like Star Fox. Leon and Katt also turn against Wolf, although reluctantly.
Fox, Falco, Krystal and the rest head for Sauria, after noticing that all of Papetoon´s forces have been destroyed. There they notice Pigma, now as a cyborg, is leading the test operation and has almost wiped out the Walled City entirely. Krystal is severely angered at this, and even more when Pigma mentions that the first prototype was used years ago to destroy Cerinia. He also mentions his and Oikonny´s current master as the one who he was supposed to hand over the Aparoid Core Memory years ago to. A fierce battle on land and sky commences, and Fox manages to defeat Pigma. Krystal, overcome by vengeance and anger, also destroys most of the invaders, but eventually doesn´t let them get the best of her and saves Fay from crashing, who she previously had argued with on several occasions. After this incident, the Star Fox team puts back their team spirit and heads on to Sector X, where the weapons are being manufactured.
As they arrive, the team splits up. Fox goes to find Oikonny, as his friends destroy the machinery. After entering the command ship, Fox is confronted by Panther. Panther taunts, humiliates and captures Fox, throwing him into a cell where Wolf and a regretful Katt already are. Leon also shows some concern, but Panther manages to convince him to stay with him. After several arguments and suspicions, Wolf manages to free the trio and helps them escape. After meeting up with the group, Lucy and Krystal have managed to recover the plans from Panther. They also have overheard of Oikonny talking to his master, who is referred to as "the Experiment 64". They contact General Peppy, who suddenly remembers hearing about this and hiding the recording to the currently destroyed headquarters of the original Star Fox team on Katina. However, he still remembers where it is and sends the team there. Wolf is also offered to join them, but he refuses.
After battling more of the superweapons on Katina, Fox finds the recording. It is revealed that Andross used the life energy from James McCloud to create a perfect clone with all of his fighting skills and Andross´ own genius mind. Fox is shocked of the thought, but after some encouraging from his teammates, he departs to Venom, where Oikonny has been gathering all of his forces to attack Corneria.
All the forces of Corneria unite to fight off the fleet. Slippy is injured, Bill sacrifices himself and Lucy almost dies as Fox manages to enter the central command in order to sabotage the superweapons. Panther is there with Leon, and holds Fox at gunpoint again. Suddenly, Wolf arrives and saves Fox. Leon turns against Panther, only to be strangled to death by him. Angered at the death of his long lost comrade, Wolf challenges Panther to a duel as Fox goes onward to the Venom Base. During the fight, Panther and Wolf have a showdown of ethics, with Panther questioning Wolf´s way of thinking, preferring his own to it. Eventually, Wolf disarms him, and Panther falls down a reactor shaft to his death after trying to attack him again. Wolf quickly destroys the superweapon controls and returns to the battlefield, where Krystal and Falco are fighting Oikonny.
Fox enters the base, and meets the Experiment 64. He tries to intimidate Fox with illusions resembling his original confrontation with Andross before engaging him in a dogfight. They are evenly matched, yet Fox manages to overcome his fears and doubts, destroying James´ evil clone. The base starts to explode, as the praising voice of the real James McCloud guides him out of there. Oikonny is also defeated, Lucy and Slippy are all right, Wolf is impressed and both Krystal and Falco managed to finish a fight completely without Fox´s help.
A huge celebration is thrown in Corneria, where everyone is rewarded with a Medal of Honor, even Wolf and Lucy, who now joins Star Fox as their seventh member. Krystal also accepts Fox´s proposal of marriage. However, Wolf throws away his medal and refuses to join Star Fox, appealing to that he wants to roam the galaxy free, now without a life of crime. Both he and Fox forgive each other for their past, and share a farewell. Katt, who also wants to be a free soul (although she and Falco made up their past arguments as well), joins Wolf as they both depart Corneria happy.