The official Japanese Star Fox 64 guidebook reveals that Pigma Dengar, who became a subordinate of Andross, was effectively the real mastermind behind the creation of Star Wolf: he goated and manipulated Wolf into becoming its leader and also working for Andross as a means to combat the newly formed Star Fox team led by Fox McCloud, taking advantage of Wolf's supposed honorable, "magnaimous" side and also his prior rivalry with Fox's father, James McCloud. It is said that he manipulates the entire team behind the scenes in accordance to Andross' orders. It also reveals that Pigma had already been working underneath Andross during his time as a researcher at the Corneria Defense Force Scientific Research Institute. It's also revealed that both Pigma and Andross had custom engineered the Wolfens that the Star Wolf team utilize in their battles against the Star Fox team's Arwings.

In Super Smash Bros. 4, the trophies for Pigma and the Wolfen would reiterate this information, as would the official guidebook for Star Fox Command. The Star Fox 64 Official Player's Guide would similarly allude to Pigma being the root cause of Fox and Wolf's rivalry, claiming that, without his influence, perhaps they could have been friends in another timeline.

Star Fox Adventures primarily takes place on a planet filled with dinosaurs known simply as "Dinosaur Planet". It would return or be referenced in future games like Star Fox Assault and Star Fox Command, as well as "Star Fox Zero - The Battle Begins", a promotional anime released to commemorate the release of Star Fox Zero, but it would instead be referred to with a different name: "Sauria".

It turns out Rare had always intended Dinosaur Planet's real name to be Sauria, as leaked voice clips from the implied climax of the original Nintendo 64 Dinosaur Planet feature the Krazoa name dropping it as they begin the alignment of the "Majestic Eight" planets to wreak havoc on the universe using the power of their god, the Quan Ata Lachu. An edition of "Ask Uncle Tusk" on Rare's old website revealed Dinosaur Planet's name to be Sauria as well.

Prior to Star Fox Zero, there were two attempts in previous installments to revitalize the concept of the Walker from Star Fox 2, or at least the idea of the Arwing transforming into a robot form, those specifically being Star Fox 64 and Star Fox Command, games that both aimed at preserving ideas from the then-long-lost Star Fox 2.

• For Star Fox 64, according to Shigeru Miyamoto in an interview at the end of the Star Fox 64 Official Player's Guide, he wanted to have the Arwing transform into "a human-type craft". This was rejected by other staff members of the SF64 development team. In response, Miyamoto told his team to come up with better ideas, and from there they created the Landmaster and Blue Marine for additional vehicles.

• For Star Fox Command, according to Takaya Imamura in an interview in 2007, the dev team experimented with having the Arwing and other spacecraft transform into robots, but this was ultimately dropped.

Katt Monroe, a female feline character who first appeared in Star Fox 64, had undergone a notable change in appearance from that game going into Star Fox Command, most notably now having black fur instead of pink. According to Takaya Imamura in a 2011 Nintendo Dream magazine interview, he changed her appearance to be more "fashionable".

Takaya Imamura, who was in charge of Star Fox Command's characters and storyline, originally wanted to do a single linear narrative similar to the campaign in Star Fox Assault. Dylan Cuthbert, the game's director (and previously the programmer for the SNES Star Fox games), convinced him to turn it into a branching storyline with multiple different pathways and endings. According to Cuthbert, this approach was inspired by old 'Choose Your Own Adventure' books, such as the "Fighting Fantasy" series.

On the Japanese website for Star Fox 64, Slippy mentions certain background characters who would appear in future installments:

• Peppy's wife, Vivian Hare. According to Slippy, Peppy took her to planet Zoness for their honeymoon, which explains why Peppy is so distraught at its polluted status in SF64. Vivian would appear in-game for the first time in Star Fox Command, where it's revealed that she and Peppy had a daughter named Lucy, and that Vivian had died of a disease several years prior.

• Slippy's father, Beltino Toad. According to Slippy, Beltino works as an engineer for Space Dynamics, the manufacturer of the Arwing and many of the other vehicles the Star Fox team utilize. Beltino would later appear in-game for the first time in Star Fox Assault, and would later appear in Star Fox Command.

It's worth pointing that unlike Vivian, Beltino was mentioned in western ancillary SF64 material, that being both the official western Star Fox 64 website and the Star Fox 64 Official Player's Guide, where it states that he helped his son Slippy create the Blue Marine.

According to Takaya Imamura in a 2011 Nintendo Dream magazine interview, frogs in the Lylat System are born as tadpoles and remain as such until they're a month old. He even explains that Slippy and Amanda's baby seen in the "Slippy's Resolve" ending in Star Fox Command was one month old already, hence why it appears as a frog. Imamura would later illustrate this fact in comic form to commemorate the release of Star Fox Zero.

One of Star Fox Command's most infamous endings see Krystal ousted from the Lylat System and becoming a bounty hunter named "Kursed" in another galaxy. Looking at the Japanese script however, reveals a slightly different story:


A direct translation of this into English would be:


It shows that Krystal instead renames herself to クラゾア (Kurazoa), which translates to Krazoa.

This is clearly a reference to the ancient tribe that once ruled Dinosaur Planet in Star Fox Adventures, similar to how her spacecraft is shaped and named after the CloudRunner tribe from that game.

Two of the game's endings make references to the F-Zero series. In the first ending, "Goodbye Fox", Falco Lombardi can be seen wearing a pair of boots that belong to F-Zero's Captain Falcon. In another ending, Fox and Falco are seen entering the "G-Zero Grand Prix", a mock up of the F-Zero Grand Prix. What's more, the two convert their fighter ships into racing vehicles, as did a character in the F-Zero games known as James McCloud, himself a tribute to James McCloud of the Star Fox games.

Octoman from the F-Zero series appears as one of the bosses in the game and a member of the Anglar Empire. His design is more reminiscent of his appearance in F-Zero: GP Legend.