Douglas Falcon begins his career in the Internova Police Force, hunting down criminals and bringing them to justice. While Falcon is a calm, collected, and merciful officer, his partner, Samurai Goroh, is much more chaotic, going to great lengths to capture their targets. Against the wishes of his superiors and his partner, Goroh continues to be a reckless officer.
Eventually, Goroh is dismissed from the Force, but not before he gives parting advice to Falcon: "Sometimes, in order to bring justice to the world, you have to cross the line."
Without a partner, Falcon becomes a lone wolf officer, and he begins wondering if he's leading a fulfilling life himself. Falcon thinks back to his late father, who was a renowned racer in the F-Zero races. Despite never wanting to be a racer, his father insisted that one day, he would be an even better racer than he was.
One day, Falcon goes to investigate a gang-related murder case to uncover something shocking: Goroh has been murdered. Angered by his friend's death, he hunts down the killer, and accidentally kills him. From that point on Captain Falcon refuses to use his blaster. Falcon learns that the gang responsible for the murder is also creating rigged F-Zero machines that are extremely fast - and dangerous. Falcon, wanting to bring justice to this group personally for what they did, decides to become an undercover racer, and finds his father's old racing helmet and his F-Zero machine, the Blue Falcon. (This suit resembles Captain Falcon's look in the SNES game)
Now known as Captain Falcon, he finds a retired F-Zero racer to train him. After weeks of preparation, Captain Falcon arranges a secret race with members of the gang, where he strikes a deal with them: Whoever wins the race will get the other racer's machine. The gang pits Captain Falcon against the best racer in their ranks, who uses the Fire Stingray. Their racer beats Captain Falcon easily, and after the race, reveals himself to be his former partner, Goroh, who has now turned to a life of crime. The gang members proceed to take the Blue Falcon and attempt to kill Captain Falcon to hide evidence of the deal, however Goroh stops them, stating he wants Captain Falcon to become stronger so they can have a true race.
At first Captain Falcon is unsure of what he's fighting for, however, he decides to continue to pursue the criminals, making a new racing suit and, with the help of his mentor racer, builds a new and improved Blue Falcon to take them on. (This suit resembles the modern look)
Captain Falcon trains rigorously to be able to match the other racers. Eventually, he finds Samurai Goroh in his gang's base, the Red Canyon, and challenges him to a rematch. Goroh reveals that he has long had a strong jealousy of Captain Falcon in the force, and this jealousy was made even more intense when he learned that Falcon became a racer like a father. Captain Falcon soundly (and I do mean soundly; F-Zero machines are quite loud) defeats Goroh. However, after the race, Goroh reveals to Falcon that his gang is working with a much larger network of criminals all making rigged F-Zero machines to win races, lead by a man named Black Shadow. Suddenly, the gangsters steal the Blue Falcon and take it away. However, Captain Falcon manages to handcuff Goroh to a tree and takes the Fire Stingray from him, and pursues the gangsters.
Following them into the city, the Blue Falcon begins running out of fuel, and Captain Falcon manages to catch him after he crashes and reclaim the machine. However, just as he's about to apprehend the criminal, Black Shadow and the other criminals appear, and he sends them all to kill Falcon and leaves. He manages to come out on top, but Black Shadow returns to finish him off. However Goroh appears and defends Falcon, causing Black Shadow to retreat. Goroh explains that although he is a criminal and has a rivalry with Falcon, he still has honor, and decides to team up with Captain Falcon to take down Black Shadow's organization.
Captain Falcon hears about a high-profile F-Zero race that Black Shadow's gang are using to test out the rigged racing machines. Seeing an opportunity, Captain Falcon and Samurai Goroh become partners once again to win the race and take down the gang once and for all. Before the race, Captain Falcon and Black Shadow meet, and Shadow introduces Captain Falcon to one of the rigged machines, his personal machine the Black Bull.
During the race, Captain Falcon manages to stay ahead, but is being outpaced by the Black Bull and two of Shadow's henchmen. During this struggle, Goroh sacrifices himself by running the gangsters off the track, and destroying their machines and his own in the process. Powered by this action, Captain Falcon intensely races Black Shadow and wins.
When the race is over, Captain Falcon desperately goes to find the destroyed Fire Stingray to save Goroh. However, he finds one of the injured gangsters, who reveals that the engine used to make the machines is based on the Fire Stingray, and after the machines were destroyed in the race, they took Goroh and the Fire Stingray's engine to their hideout, a large building outside of the city.
Captain Falcon races after the retreating criminals to the building, where he encounters Black Shadow. Shadow announces his plan to use the prize money from the rigged races to take over the planet, and, after cursing Falcon's meddling, escapes with the engine and sends his men to kill Falcon. Falcon soundly defeats the gangsters, and proceeds to chase Black Shadow through the city, cornering him at a bridge. Captain Falcon and Black Shadow fight one on one. After a long struggle, Captain Falcon manages to defeat Black Shadow, who leaps off the bridge to avoid being imprisoned.
After ensuring Goroh's safety and jailing him, and turning over the engine, Captain Falcon quits the Internova Police Force. Black Shadow turns out to have lived through their last encounter and now has a huge bounty on his head - a bounty that Captain Falcon decides to hunt personally.