WARNING: The following contains spoilers for Chapter #52, “Baryon Mode,” of Boruto: Naruto Next Generations by Masashi Kishimoto, Mikio Ikemoto, Ukyo Kocachi, Mari Morimoto and Snir Aharon, now available from Viz Media.
Isshiki's sinister journey to claim Kawaki for his own has been a very frustrating one in the Boruto manga. He engineered the teen to be a perfect vessel so he could be reborn in it, achieving his full potential on Earth, but things haven't gone according to plan, with Kawaki being taken in by Naruto.
When Isshiki finally manifested in Jigen's body and came for the kid, it seemed like Naruto and Sasuke would be able to get the upper hand by taking the villain to a secret dimension to kill. However, Chapter #52 has now confirmed Naruto may well have doomed Kawaki thanks to a gift he gave him weeks before. In the process, Isshiki is set to get everything he ever wanted.
When Naruto fought Kara's Delta, Himawari got in the line of fire. Luckily, Kawaki would risk his own life to save them, losing his arm in the process. After Delta was sent back licking her wounds, Naruto's science team tried to create a prosthetic arm for Kawaki but it wasn't easy given his unique DNA. Luckily, Naruto had one to offer as he lost his arm years ago fighting Sasuke, and apart from it being fitted to Kawaki, Naruto blessed it with his chakra.
It was all to help Kawaki heal, but it acted as a tracker for Naruto and Kurama, the Nine-Tails Fox, inside him to keep an eye on the kid as he bonded with Boruto and Co. Now, though, that has turned into a problem because while Amado and Shikamaru's team hid Kawaki away for a bit, the arm has become a marker giving Isshiki the location of the boy.
It occurs when Isshiki battles Naruto's Baryon mode, where their chakras mix. Naruto's draining the villain but this allows Isshiki to connect to this new chakra the Hokage and Kurama have cooked up, and he begins sensing the chakra in Kawaki's arm. As a result, Isshiki uses his ocular jutsu, locks onto Kawaki and pulls him into the dimension. Naruto's act of kindness has now gifted Isshiki the perfect weapon.
All of Sasuke and Boruto's hard work is now set to be erased. They knew if Isshiki found the teen, he could implant a new Karma mark on him and begin the process of manifesting again with way more power than before. If Naruto expends a lot of this Bayron energy to save Kawaki, his life essence will dissipate so now, Isshiki has the full advantage. This implies Isshiki will take over Kawaki's body. The scene at the start of the series, when "Kawaki" boasted to an older Boruto about destroying Konoha and killing Naruto, may well be showing Isshiki in his younger form.