The plot to Star Fox: Farewell, Beloved Falco. It is set four years after Star Fox 64 and four years before Star Fox Adventures, since Adventures takes place eight years after Star Fox 64. It revolves around the past life of Falco Lombardi, how he came to be separated from the Star Fox Team, and how the team are starting to go broke after many years of peace in the Lylat System.
Four years after the Lylat Wars, the Star Fox team, due to the peaceful times, were largely out of work. Fox has now become easily frustrated, Great Fox is in a very sorry state and even Slippy is barely able to keep up with the necessary repairs. Falco is now more uncooperative than ever and even worse is finding entertainment in fighting with Fox. Peppy has now retired and does his best to keep an eye on everyone, but even he can't perceive the relationship between Fox and Falco. During a training session between Fox and Falco on Arwing piloting via GBC handheld simulators, the Star Fox team receive a S.O.S. transmission from Katt Monroe regarding her as well as her gang, the Hot Rodders, being attacked by an unseen assailant. She seemed to be in great distress as her transmission had cut in the middle of her sentence, so Fox asked ROB 64 to track where the message came from, where he reveals it to be Titania. Falco then tells Fox that he's having himself a vacation and immediately departed for Titania, despite the protests of his team. Most of the team had to discuss on the matter, as Peppy noted that Katt did not possess a stellar record, however, Slippy was more sympathetic and felt her cries for help seemed pretty genuine and they set Great Fox's course to Titania after Falco.
ReunionUpon arrival on Titania, Falco saved Katt Monroe from a Goras. Katt then thanked Falco, although Falco advised her to leave immediately, as the Goras had only retreated. Afterwards, the Star Fox team, searching for the currently AWOL Falco, arrived at Titania, where they landed at one of the research bases established after the Lylat Wars to research ancient planetary history. Upon completing docking clearances, the base's commander, Captain Shears, introduced himself. Upon learning of the Star Fox team's situation, he agreed to help them find Falco, although under one condition: they retrieve some of Andross's research that was allegedly stolen by remnants of Andross's Empire.
Meanwhile, Katt explained to Falco that Shears issued a manhunt, and she suspsects that Shears is planning to do something bad after the Hot Rodders stumbled on research documents. Falco and Katt then catch up on each other's lives, where the latter reveals that she's now romantically involved with someone who isn't Falco. Ultimately, after being briefed on the situation, the Star Fox team agrees to the mission. Shears then shows them the Venomian ship responsible for the thefts: A ship that also happened to be the Hot Rodder's ship. On the bridge of the ship, the Hot Rodders are excited at the prospect of Falco being among them. However, they are suddenly attacked by the Star Fox team. Falco then battles against the Star Fox Team, fighting Fox in particular. Fox, forced into a dogfight, then participated in it. Falco then fires a charge shot that severely damages Fox's ship, although Falco nonetheless sustained significantly worse damage, eventually crash-landing in the Titania desert.
In the aftermath, Fox, while recovering in the Great Fox's medical bay, is scolded by Peppy for the foolish actions. Slippy expresses concern for Falco, noting that he sustained the worst of the damage. Afterwards, Peppy then asks what led to the dogfight, to which Fox reluctantly tells him about Falco's apparent defection to the Venomian army. Falco is later revealed to have survived, although his Arwing is damaged in the middle of the desert, forcing him to undergo repairs. He does nonetheless express his admiration for Fox's skills.
Meanwhile, Shears learns that the Star Fox team failed to stop Katt's team. Shears grows concerned, realizing that his project will most likely be leaked, and he'll most likely end up suffering a tribunal, then orders for the Goras to be deployed once again, this time to take a hostage. Peppy, upon learning Fox's reason, is disturbed at the implications of what is going on. Now finding Shears to be quite suspicious in his request for evasive actions because of the apparent silence around the base after being supposedly in danger, Peppy has Slippy try to investigate via scouting the base via Landmaster, as Peppy himself is too old to go into active duty. Slippy does so reluctantly, as he had once been shot down on Titania and nearly made into a Goras lunch. No sooner than he started recollecting this traumatic event did the past strike back in the form of the Goras.
Eventually Peppy started to regret sending Slippy out on his own after not hearing from him for so long, but Fox felt Slippy would be fine seeing as he did manage to pilot his own Arwing during the Lylat Wars. ROB then tells them that they are receiving an incoming transmission from the ship that was supposedly the Androssians. Afterwards, Katt's ship, still believed to be the Venomian remnant's ship, hailed the Star Fox team. Katt then angrily chews out Fox for apparently killing Falco, with Fox expressing surprise that Katt was apparently on Andross's ship. Katt and her second in command, Cool, then reveal that they weren't even affiliated with Andross. Peppy then has Cool explain his team's actions: The Hot Rodders had earlier stumbled upon some research documents at Shears' lab, and stole the documents with the intention of selling it to the highest bidder. They never opened the files, so they never even knew just what was in the documents. Peppy then orders ROB to analyze the files. After ROB concluded his analysis, ROB revealed, to Cool's shock, that there wasn't any weapons development inside the files: Instead, it was DNA coding for a cloning project regarding the resurrection of Andross himself, to the team's horror. Peppy then realizes that he had inadvertently put Slippy in grave danger, and tells ROB to call Slippy back. ROB, however, reluctantly informs Peppy that he lost Slippy's contact a few hours ago. Slippy then wakes up inside a cell inside Shear's base. The Star Fox team and the Hot Rodders, in a joint effort, proceed to prepare a rescue operation for Slippy, where Fox will infiltrate the base, while the Hot Rodders will cause a distraction by "making noise." Katt still harbored somewhat of a grudge for Fox's defeating Falco, but nonetheless complies, realizing its to their mutual benefit.
Infiltration and Rescue
Meanwhile, Shears, upon learning of the full front, realizes that the Star Fox team most likely knows what he's up to, and realizes he can't allow them to live. Fox, under Peppy's guidance via transceiver, locates Slippy's cell, although he inadvertently gets spotted by some of the guards, forcing him to locate Slippy and run away from the guards. After finding Slippy, they duck into a room to elude the guards and seal themselves in. Unfortunately, it turns out the room was actually Andross's cloning chamber. The growth progress seems practically complete with Slippy expressing fear that he'll eat them. Shears then reveals himself, and Fox attempts to stop Shears. However, a Titanian River Boar, Shears' steed, intercepts Fox, and Shears then expresses shame that he has to silence Fox. As Fox and Shears battle, Slippy attempts to halt the rejuvenation process. Andross then briefly asks who Slippy is, causing Slippy to think he hasn't regained his full memories yet. However, the clone sees Fox, and remembers who Fox is.
Base ConflictMeanwhile, Katt and the Hot Rodders manage to wipe out most of Shears' men, only to encounter the Goras. Katt, remembering the day Falco left and his harsh final words to her, decides to take it on by herself and tells her group to leave. However, Falco manages to arrive at the last minute, and proceeds to fight the Goras, finishing it off for good by ramming into it, vivisecting it. Falco then smiles after he notices that Cool might be forming a romance with Katt after he saves her from being crushed by the deceased remains of Goras. Fox and Shears continued their fight all the way to a ceremonial room. Fox then uses part of the room's coat of arms to fight even-handedly against Shears. He eventually manages to disarm Shears with the coat of arm's rapier, destroying Shears' own rapier. Slippy, unfortunately, was unable to stop the rejuvenation, and in fact inadvertently sped it up.
Return of Andross
Andross, having regained his memories of his death, declares his hatred of Fox in such a way that he destroyed his containment tank, drenching Slippy in culture fluid, who then attempts to warn Fox. Shears then attempts to escape on his steed, only to end up crushed by Andross. Andross then attempts to inhale Fox upon declaring his intention of killing Fox. Fox then proceeds to throw his rapier into Andross's left eye, destroying it and briefly diorienting Andross. Slippy and Fox then discover the impounded Landmaster. Left with no other option, Fox fired a supernova bomb at Andross just as Andross located them, destroying the base and nearly themselves in the process. Afterwards, Falco contacts Fox and tells him that he is retiring for a while, and tells Fox to tell Katt to retire from the Hot Rodders and do some lawfulness for a change. After Fox tells Katt Falco's final transmission, Katt thanks Falco.