WARNING: The following contains spoilers for Sasuke Shinden: The Teacher's Star Pupil by Jun Esaka and Masashi Kishimoto, available in English from Viz Media now.
Boruto hasn't treaded much water in terms of terrorist organizations, apart from Kara, Jigen's sinister cell. It's definitely the franchise's way of differentiating itself from its predecessor, Naruto, which focused a lot on the Akatsuki, the terrorist antagonists of much of Shippuden. However, in the novel Sasuke Shinden: The Teacher's Star Pupil, introduces a deadly new sect known as the Purple Moon -- a religious cult, while not as powerful as the Akatsuki or Kara, that still the tools to bring down powerful nations.
At the start of the novel, Sasuke's investigating the purple-clad ninjas that bombed the Thunder Train just outside of Konoha. Upon seeing so many of them kill themselves upon defeat, Sasuke becomes very worried. Eventually, the Ranger returns to Konoha and, after digging up some information, arrests the pop star known as Lily.
He exposes her earring, which is a mark of the Purple Moon -- naturalists and extremists from the Land of Water. While this nation has joined Naruto's alliance and respects Konoha and the Land of Fire in general, the Purple Moon are a purist segment and rogue faction. They don't believe in ninjutsu but deriving their abilities from nature -- i.e. the moon. They got their name because of how the moon looks in their waters, which to them is the symbol they wear to fight the progress Konoha's pushing.
All the Great Nations are now using science in their societies and the Purple Moon see this evolution as impure, thinking these regions are leaving nature behind. So, they've resolved to strike at the heart of the alliance, cutting off the hydra's head so these forward-thinking philosophies are stopped. It's why Lily's dad, the group's leader, kept them isolated from the rest of their people, similar to the Uchiha in Konoha. He instead raised her and harnessed her abilities to control people's bodies using bio-electric shocks, hoping she'd go to Konoha, infiltrate and lead attacks on the Hidden Village.
No one would suspect Lily for the bombings, which would prove Konoha's instability. The bad PR and Konoha's inability to solve the problem would further mark Naruto as an unfit leader, hopefully inspiring other nations to stop following their lead. However, Lily doesn't endorse murder and chose instead to go as a pop star, making Konoha's seniors -- like Sasuke -- look aggressive and to show that, if accidents occur at her shows, clearly Konoha can't lead the alliance. Her dad didn't like these pacifist ideas, though, so when she defected, his goons came after her on the train and at the show that Sasuke interrupted.
Still, Sasuke has no sympathy, as both methods bring disgrace unfairly to Konoha, undoing what he and Naruto worked so hard to achieve. Sasuke would later learn Lily's dad was one of the shinobi who died on the train and, when they stop her other mission of blowing a boat up outside Konoha, she goes on TV and repents. The fact Sasuke and Boruto save her from the explosion at the port is enough to change her. The way Naruto easily forgives her and gives her air-time knowing she could easily sully Konoha's name proves to her that her cult is indeed wrong about the alliance's ambitions. Lily realizes she needs to get the remaining cultists to shed their old ways and join with the rest of the Land of Water so they can be part of a first-world initiative meant to improve everyone's lives.