For WMG regarding the entire franchise, go here.
James is actually James Bond Sr's son
Come on! This is James Bond we're talking about. The "nephew" part is just a ridiculous lie probably to keep the boy safe. (Not that it works very well.)- It's a lie to keep the censors happy.
- Not to mention, in the novels Bond does have a son: James Suzuki, whose mom is Kissy from You Only Live Twice. So James Bond Jr. being a second Bond illegitimate child wouldn't be that farfetched.
- Since James Suzuki is killed off in the books, this has rather dark implications about what happens past the end of this series.
The older James Bond really does have a brother, the father of JB Junior.
Officially this brother is not supposed to exist, in large part to shield 007 from blackmail, that is, the threat of having anyone harm his family. Bond's brother either goes under another identity and/or lives off the grid. That doesn't mean he's not important either; if the Bond family has links to Scottish nobility this unseen brother may be helpful in pulling a few behind-the-scene diplomatic strings. Of course the passion for spying is probably in the Bond blood, and young James couldn't help hearing about his famous uncle.- Turns out he's the son of the title character in Operation Double 007 who was played by Sean Connery's brother, who in the film was heavily implied to be James Bond's brother, making Operation Double 007 in continuity with James Bond Jr.
James Jr. is Aunt Charmain's grandson
This is the most boring of the possibilities, but both the novel and film Bonds acknowledge an aunt, named Charmain in the books and sarcastically described as being "tall, dark and handsome" in The Man with the Golden Gun, who is Bond's closest living relative. James Jr. wouldn't necessarily be surnamed Bond but might just call himself that to invoke his more famous first cousin once removed. James is the NEXT James Bond
A popular theory about the film franchise is that its use of The Other Darrin is in fact more of a The Nth Doctor; all those different looking Bonds are completely separate people, with the code name "James Bond" being passed down when one of them dies or retires. And here we have a kid using that name and training as a secret agent while still a teenager. Coincidence? He's actually being groomed as the next replacement Bond.- That explains "Uncle James" teaching him "the game".
Goldfinger is Goldfinger's twin brother
The original script for Diamonds Are Forever had Goldfinger's twin brother out for revenge. This can explain why he is still alive. He's not. It's his brother.- In that case, which one is Goldie's father?
Scumlord is Ernst Stavro Blofeld
Well it does make sense, considering he's the closest thing Bond had to an archenemy. SCUM is merely a subdivision of SPECTRE, same as QUANTUM.
Spectre established that numerous smaller organizations such as QUANTUM acted as proxies for SPECTRE and its head agents itself. SCUM, being an organization limited to this series, could easily fit into those subdivisions.
James is the nephew of the Sir James Bond (the one played by David Niven)
They named him after the retired version of 007 in Casino Royale (1967). After all, what would the censors go with? A "sex maniac who dragged the James Bond name through the dirt"... or the retired upper-crust guy who made that quote? James Jr. is a regeneration of James Bond
Roger Moore left the franchise after A View to a Kill after he found out that he was older than Tanya Roberts' mom... in the fiction, if Bond found out similar information, he could psychically guide his next regeneration to be younger (the same way the War Doctor went through the progressively younger Nine, Ten and Eleven after dealing with his grief). He unfortunately made his regeneration too young and MI-6 forced him to be "Junior" until he visibly aged a bit.