Warning: Spoilers ahead for Boruto: Naruto Next Generations Chapter 55!
The most recent big villain of losing an arm.
In Boruto: Naruto Next Generations, the very first major villain is Momoshiki, another member of the Otsutsuki Clan. The series also reveals that there isn't just one Otsutsuki, but a lot. These Otsutsukis haunt the world as they try to accomplish what Kaguya failed to do. In order to do that, Isshiki, the other major Otsutsuki, search and nurture vessels for his revival. If not for Konoha's meddling, he may already have succeeded enacting his plan. However, Lady Luck isn't smiling on him. With Naruto, Sasuke, and Boruto helping him, Kawaki finally ends Isshiki once and for all.
All throughout the series, Boruto: Naruto Next Generations has been priming fans to think that the Otsutsuki are the biggest villains in the series. While there's truth in that, Isshiki's death becomes a factor to something that may be bigger. Using the last of his existence, he materializes using Code's failed Karma. He personally tells him about his doom and how it happened. But instead of sweet farewells, Isshiki es the will of Otsutsuki to Code instead.
Isshiki teaches Code how the Otsutsuki Clan absorbs the planet's chakra. He also tells him that even though he is human, he can cultivate the Divine Tree by feeding either Kawaki or Boruto to the Ten-Tails. According to Isshiki, Code can become a true Otsutsuki once he's eaten the Chakra Fruit that the Divine Tree will bear. At the end of the chapter, Code even contemplates who he is about to hunt.
With such an unexpected twist, fans have no idea how much threat Code actually poses at this point in time. Even though Isshiki refers to himself as a loyal servant, he doesn't have the opportunity to show the readers his true value. Nevertheless, this means that there are threats in Boruto: Naruto Next Generations other than the Otsutsuki.