WARNING: The following contains major spoilers for Boruto: Naruto Next Generations #47, by Masashi Kishimoto, Mikio Ikemoto and Ukyo Kodachi, available now in English from Viz Media.
The Boruto manga has found Naruto and his Konoha council struggling to prevent Kawaki from channeling the evil Isshiki Ōtsutsuki, terrorist chief of Kara. While the Karma mark doomed the young shinobi to the alien's inevitable possession, it also allowed fans to breathe a sigh of relief, as the mark meant the villainous Kawaki seen at the beginning of the series might have just been Isshiki in his body.
However, thanks to Boruto #47, following Amado's 'war cure,' Kawaki is saved from being a host. However, this means that he really will become Konoha's enemy and the four-year flash-forward of Kawaki aiding in the village's destruction will somehow come to pass.
Amado manipulated the ninja as part of a long-term plan to buy time and weaken Isshiki, who was trapped in the body of the monk, Jigen. He played Jigen against Konoha and, following the villain being weakened by Naruto and Sasuke, Amado had Koji Kashin turn on his leader to kill the Kara head for good. However, they both knew Koji couldn't kill an Ōtsutsuki -- the battle was a planned move so that Koji could destroy Jigen's body and weaken Isshiki by forcing him to reincarnate using the corpse.
Amado's main play here was forcing Isshiki come to light before Kawaki was fully ready as a vessel. Once Koji burns up Jigen, Isshiki finally emerges, though he desperately wanted to wait until Kawaki -- the perfect body -- was complete. However, despite the less-than-ideal body, Isshiki is still a powerful enemy, and so Amado's in Konoha testing another theory to weaken the alien.
Though he lacked proof, Amado gambled on that, once the Karma mark activated on Jigen, the ones on other vessels like Kawaki would be erased. His bet pays off in that, while it's a painful process, the mark fades from Kawaki, freeing him of Isshiki's influence. However, this development makes whatever set Kawaki on the path to destroying Konoha even more mysterious. In the original series, Sasuke broke bad because he wanted revenge, but it's different for Kawaki. Naruto's family has adopted him and the village has protected him. He's in the right place with the right people.
Admittedly, some folks, like Shikamaru, are still skeptical, but that's only because Kawaki was marked by Isshiki, making him out to be an untapped weapon. Now, with the mark -- and the distrust it created -- gone, it's anyone's guess as to what makes him turn on his new family. Inthe flash-forward, Kawaki claims to have killed the Hokage, but how he got enough power to do so is yet another mystery. Amado's plans for the teen could extend beyond the seeming goodwill of eliminating Isshiki -- he could have his true sights set on the destruction of ninja everywhere, and use Kawaki to do it. Konohagakure is in grave danger, but there's no indication why Kwaki would want to destroy the place that's given him everything he's ever wanted. As it stands, Boruto thinks he's gotten his friend back, but it's just a matter of time before it all comes crashing down. Kawaki's liberation is set to destroy everything Naruto worked for.