Borderlands 3 was the long-awaited follow-up to Borderlands 2 and is one of the best feeling first-person shooters of the year. Unfortunately, the game left much to be desired with its cookie-cutter story that doesn't hold a candle to the story of its predecessor.
While it sets up and follows through on its main storyline, it leaves plenty of loose story threads, some of its own and some leftover from the earlier entries in the series. While we are probably very far from the next main entry in the series, there are plenty of loose storylines left to be wrapped up.
10 The Watcher
Borderlands: The Pre-Sequel gave tons of backstory and lore for the Borderlands universe but it also set up the next entry at the very end of the game. The Watcher shows up and stops the execution of Athena, telling Lilith and company that they would need as many vault hunters as they could get for the upcoming war. This is not referenced even once in Borderlands 3 nor does the game feature a large scale war that requires that many vault hunters. Must have slipped Lilith's mind.
9 Rhys and Dahl
The vault hunters leave Rhys in decent shape after helping fend off a hostile takeover by Maliwan. Rhys revived the near-dead corporation with money he presumably acquired from the vault he entered in Tales From the Borderlands. The exact state of Dahl, however, is a mystery, since the corporations suffered substantial losses, both in reference to money and personnel. It will remain unknown if the company can recover from this event and continue to thrive, but since Rhys is one of the good guys, its probably got a good shot.
8 Maliwan Sibling Issues
On the flip side of the attempt corporate take over Maliwan, one of the main gun manufactures in Borderlands, might be in some rough shape after getting put in its place by the vault hunters. With Katagawa Jr. now dead, this leaves some room in the company on an executive level.
While his parents are still above him, most likely in charge, the only remaining sibling of his he didn't kill, Naoko is still alive despite being thought dead. It's unclear how long it will be till it's her turn in charge, but that would put the leader of Maliwan in debt to the vault hunters for saving her life.
7 Children Of The Vault
The Calypso twins managed to rally nearly every bandit in the nearby universe behind them in their quest to become gods. With them both six feet underground it leaves a very large mass of mildly organized bandits and psychos without purpose. They could very easily take over Pandora and the other planets featured in the game or impose any government they pleased. It's unclear if this issue will ever be acknowledged or if the COV will continue to operate business as usual until the next title.
6 Ava
Love her or hate her, Ava has been bestowed Maya's siren powers but not without the lingering pain of Maya's death. While Ava reacted poorly during the main story, blaming and raging at Lilith and company for not going headfirst at the twins immediately following, it's not clear at the end of the game if she has come around with her grief, or if the pain will build into something more villainous. Ava may have been training to be a vault hunter but the tragedy could mold her into something more sinister.
5 Dr. Zed
Unless he decided to take the money from his vending machines and retire, Dr. Zed is just flat out missing the entirety of Borderlands 3. Now, it isn't totally insane that a character would not be directly involved in the main story, but it's odd in his case.
Every other staple character from Sanctuary is present and there is a medical bay on the ship, which is occupied by Tannis, who isn't that kind of doctor. This absence is an unresolved story thread for sure but there isn't much to go off from to even start trying to find him.
4 Tales Canon
This one is much more complicated, but we still don't know what choices in Tales From The Borderlands are canon. Some of the characters, like Vaughn and Rhys, are very much present in Borderlands 3 but Fiona and Sasha are not. There are other big points, like if Rhys chose to destroy the Handsome Jack AI that he acquired during the game. A sentient Handsome Jack could cause a ton of mischief for the vault hunters but we don't know if he still exists.
3 Jakobs Ownership
Do you gain ownership of a company stolen from you if the current owner is killed? That might not be totally out of place in Borderlands but it's never explicitly said if that's the case. It's unclear how the company was even stolen in the first place but the current state of the Jakobs corporation is unclear. It's also unclear why Sir Hammerlock would leave Eden-6 after getting reunited with his significant other just to feed contracts for large animals to the vault hunters. It's pretty strange.
2 Lilith's Powers
So it's very unclear if Lilith has died at the end of Borderlands 3 she flys into the moon and explodes into a fire hawk symbol but the other characters make it seem like she might be alive.
Something pointing to the possibility that she may be alive is that we don't know of any characters who have inherited her siren powers. Based on the story, the powers manifest in whatever character the plot needs to gain powers. In addition to that, Troy's and Tyreen's powers should find a new home as well but who even knows anymore.
1 Zer0
What is Zer0's deal in this game? It seems like he is just friends with Rhys and helping out Dahl as a favor since he is never referenced as being hired or paid. It seems odd that once it is semi-dealt with he bounces out to ride around on Sanctuary 3 giving out kill contracts to vault hunters for anybody and everybody. He also does this without ever directly interacting with the vault hunters so it's not like he physically needed to leave Rhys. It's unclear what his goal or purpose is but this could also just be to serve the gameplay.