Although the Star Wars prequel trilogy involved a lot more pre-planning than the sequel trilogy, there were still a handful of unanswered questions and unresolved storylines along the way. In some cases, George Lucas established plot threads that he ended up dropping in order to streamline the story and focus more on Anakin’s journey.
Either way, as much as the prequel trilogy holds up as a complete piece of storytelling, there are a couple of plot threads that went nowhere. While all the major storylines got paid off in a mostly satisfying way, a few of the minor ones didn’t.
Kamino’s Removal From The Jedi Archives
After the release of Attack of the Clones, when George Lucas was already working on the script for Revenge of the Sith, he promised Star Wars fans that the third prequel movie would answer the mystery of Kamino’s removal from the Jedi Archives.
However, as he actually dug into Revenge of the Sith, he decided to drop the Kamino mystery in favor of refocusing the narrative on Anakin’s dark path.
Droids’ Memories
At the end of Revenge of the Sith, C-3PO’s memory is wiped, explaining why he doesn’t tell Luke and Leia that he used to belong to their parents, but R2-D2’s memory remains intact.
In the original trilogy, R2-D2 doesn’t recognize Yoda when Luke takes him to Dagobah, and he doesn’t tell Luke that he used to hang around with his father, and that his father is Darth Vader. So, how exactly do droids’ memories work?
The “Chosen One” Prophecy
When Qui-Gon discovers Anakin in The Phantom Menace and checks his midi-chlorian count, he’s over the moon (or over the forest moon of Endor) to have discovered the prophesied “Chosen One,” who will bring balance to the Force and prosperity to the Jedi Order.
But the prequels never really elaborate on the “chosen one” prophecy. Where did this prophecy come from? And what exactly, aside from an insanely high midi-chlorian count, qualifies Anakin to hold the title?
Padmé’s Political Career
At the end of The Phantom Menace, Padmé gives up her duties as Naboo’s queen in order to pursue a career in politics within the Galactic Senate. In Attack of the Clones, she’s forced into hiding by a string of assassination attempts.
Then, Revenge of the Sith ignores Padmé’s political career entirely, confining her arc to simply moping around the house until, eventually, she dies of sadness right after giving birth. This also retconned Leia remembering her mother in Return of the Jedi.
The Gungans
This one probably wasn’t a creative oversight, but rather a response to the intense hatred that the Gungans received from the Star Wars fan-base. In The Phantom Menace, Jar Jar is disavowed by his people and later redeemed in their eyes.
Boss Nass stands alongside Padmé in the final scene of the movie, celebrating their combined victory against the Trade Federation. But as Jar Jar got sidelined in the rest of the prequels, due to the fandom’s hatred, the Gungans were never seen again.
The Tragedy Of Darth Plagueis The Wise
One of the most crucial parts of Palpatine’s plan to turn Anakin over to the dark side is telling him a little yarn known as “The Tragedy of Darth Plagueis the Wise,” about a Sith Lord obsessed with unlocking the secret to eternal life who was killed by his apprentice.
It’s heavily implied that Palpatine was that apprentice, but it’s not explicitly stated. Colin Trevorrow’s original script for Episode IX involved Kylo Ren visiting Palpatine’s master, who would turn out to be a giant Lovecraftian monster, but as it stands, this storyline remains unresolved.
Sifo-Dyas
When Obi-Wan arrives on Kamino, he’s told that the Clone Army was commissioned by Sifo-Dyas, and the Kaminoans assume that Sifo-Dyas is still on the Jedi Council.
However, Obi-Wan revealed that Sifo-Dyas was killed a decade earlier, later revealed to be at Count Dooku’s hands. But after that, Sifo-Dyas is never mentioned again.
R2-D2’s Gadgets
In the original trilogy, R2-D2 barely has any gadgets. He shoots Luke’s lightsaber to him during the battle over the Sarlacc Pit and cuts through the net that the Ewoks use to trap the Rebels, but that’s about it.
In the prequel trilogy, Artoo suddenly had dozens of never-before-seen gadgets that would’ve come in handy in the original trilogy, including the ability to fly. The prequels never explained why Artoo’s tech got downgraded ahead of the Empire’s rise.
Qui-Gon Communicating From Beyond The Grave
At the end of Revenge of the Sith, Yoda tells Obi-Wan that Qui-Gon has contacted him from beyond the grave, and that he’ll be able to teach them how to do the same with the Force. However, it’s never explained how Qui-Gon managed to figure out how to come back as a ghost.
It also would’ve been great to actually see Qui-Gon’s Force ghost in the movie. There was originally a scene in which he visited Anakin to try to dissuade him from joining the dark side, but Lucas cut it.
Anakin’s Father
When Qui-Gon asks Shmi about Anakin’s father in The Phantom Menace, she implies that it was a Christ-like virgin birth. There was no father; Anakin just appeared in her womb one day. One early draft of Revenge of the Sith saw Palpatine revealing to Anakin that he manipulated the midi-chlorians in the womb of Anakin's mother in order to create him.
So, essentially, Palpatine would be revealed to be Anakin’s father. However, Lucas cut this from the script, feeling that he was just rehashing Empire’s “I am your father!” twist.