Caution: Spoilers ahead for the Boruto manga
Could Amado be the real villain in Boruto: Naruto Next Generations? Ever since Boruto's opening episode, the true enemy of the Naruto sequel has remained hidden in the shadows. Initially, it seemed that Kara was the biggest threat. Eerily similar to the Akatsuki, the Kara was a powerful group of fighters enhanced with cutting-edge ninja technology and led by Isshiki Otsutsuki, the partner of Kaguya. However, the big boss of Kara was taken down by the formidable combination of Naruto, Sasuke, Boruto and Kawaki. Isshiki swears his spirit shall live on through Code, his most loyal servant, but the flame-haired follower doesn't seem to be the overarching nemesis of the Boruto story.
The assembled quartet of heroes were only successful in defeating Isshiki thanks to the cooperation of Amado. Introduced as Kara's chief scientist, Amado is the one responsible for each Kara member's artificial power-ups. He was also in charge of Isshiki's mission to find the perfect vessel, experimenting on Kawaki with the Otsutsuki Karma mark for this purpose. Despite appearing to serve diligently, Amado betrayed Kara, and defected to Konoha Village with a plan to defeat his former master. Through Amado's cunning, Isshiki is no longer alive (physically, at least) and Kawaki has been freed of Karma.
Nevertheless, there's plenty that doesn't add up about Amado, especially considering Kawaki's dark future in the ominous Boruto flashforward. Could it be that Amado is an even bigger threat than Isshiki Otsutsuki?
Amado Remains Suspicious (Despite Helping Konoha)
Ever since Amado's defection, Shikamaru has been deeply suspicious of Konoha's new ally, and it's not hard to see why. The scientist keeps his cards close at all times, and is complicit in the numerous atrocities committed by Kara, including the deaths of many shinobi (fodder, but still...) and the manipulation of Dr. Katasuke. Amado swears his intention was only ever to protect the world from Isshiki, and he was forced to play along as a faithful Kara member until the time to strike arrived, but there are several clues to suggest Amado is lying here.
In the Boruto manga, Amado reacts strangely when the report confirming Isshiki's defeat arrives. Katasuke and Sumire notice the scientist muttering into his hand, and when the heroes arrive home safely, Amado is uncharacteristically concerned about Kawaki's welfare, desperate to know if the former "vessel" is safe. Amado has shown little regard for Kawaki previously, and combined with the mumbling, he seems to have a hidden agenda.
The latest episode of Boruto's anime supports this theory. Watching Kawaki train, Amado says to Koji Kashin, "the world will kneel before Kara." It's a weird remark to make considering Koji is Amado's ally in betraying Isshiki, and no one else is around. Arguably, the surveillance in Kara's base means Amado has to maintain the act even when he's alone or with allies, but there's no suggestion of this in the episode itself. Perhaps Amado has his own vision of what "Kara" means, but needs Isshiki gone before he can implement his true design. This would certainly explain how Amado was able to bear the ethical burden of Isshiki's horrific agenda.
Finally, it's worth questioning Amado's relationship to Konoha Village. Not only does he model Koji on a sample of Jiraiya's DNA, but Amado recognizes the current generation of Ino-Shika-Cho as soon as they confront him. Evidently, the scientist has a prior connection to the village, but no one seems to remember him living there. Amado might've left on bad terms and been scrubbed from Konoha's archives.
Kawaki Will Break Bad (& Regain Karma)
In a shocking flashforward sequence, the opening episode of Boruto reveals a future where Konoha Village is destroyed, and Naruto is dead. Boruto and Kawaki are battling, and both possess Karma marks, which they're able to wield easily. Currently, however, Kawaki is very much a protagonist - so much so, he vows to protect the Hokage with his life and has forged a brotherly bond with Boruto. Furthermore, Kawaki has been stripped of his Karma thanks to Amado's plan. For Boruto to line up with the flashforward timeline, something must happen to turn Kawaki bad and reinstall his Karma powers. Amado could be responsible for both.
Before leaving Kara HQ, Amado says the "work" can still be carried out in Konoha, but he doesn't specify what this means. Without an Otsutsuki to take orders from, there's no reason for Amado to continue the Karma experiments unless he has plans of his own for the mysterious power. And if Amado pushes forward with his research, this might explain how Kawaki regains Karma in time for the flashforward fight against Boruto. Amado has packed Kawaki's body with scientific ninja tools, and Boruto already confirmed that after holding Karma for so long, Kawaki is 80% Otsutsuki. Through his experiments, Amado might've learned how to trigger a relapse of Kawaki's Karma using technology.
The aforementioned scene where Amado marvels over Kawaki's power and claims the world will "kneel" could reveal why the Sasuke-esque character is a villain in the future. Amado clearly has his sights set on the powerful youngster for one reason or another. Perhaps Amado mentally breaks Kawaki's spirit to turn him bad, or maybe the scientist installed a secret component while working on Kawaki's body, but rather than taking him out (like with Delta's killswitch), the modification allows Amado to control Kawaki.
Theory: Amado Wanted Kawaki For Himself To Get Revenge On Konoha
Given his obvious history with Konoha Village, it's not a stretch to imagine Amado might want revenge on the ninja world, perhaps for ostracizing him, or disagreeing with his approach to scientific advancement. This might sound similar to Orochimaru's backstory, but Boruto hasn't exactly shied away from repeating old tropes.
After striking out alone, Amado eventually joined with Isshiki Otsutsuki, recognizing the other-worldly villain as his best chance of getting back at those who wronged him, since Amado himself isn't much of a fighter. But his revenge plan might've changed after encountering Kawaki. Instead of relying on an unpredictable alien seeking to destroy the entire world, Amado realized he could use Isshiki's Karma and the raw potential of Kawaki to create a fighter even more powerful than an Otsutsuki - and much easier to control.
But first, he needed to remove Isshiki's existing Karma mark on Kawaki and have someone kill his former boss before it could be replanted. By pretending to align with Naruto, Amado got his wish, and is now free to infect Kawaki with his own artificial Karma, beginning a long-awaited revenge plot using Boruto's best friend as a puppet. This would explain Amado's enigmatic behavior, why Kawaki goes bad, and how Konoha was destroyed in Boruto's flashforward.