The following contains spoilers for Chapter 71 of Boruto: Naruto Next Generations, “Hindrance,” by Masashi Kishimoto, Mikio Ikemoto, Mari Morimoto and Snir Aharon, now available in English from Viz Media.
One of the most shocking moments in the Boruto manga came recently when Amado revealed he placed a new Karma mark on Kawaki. The teen had no idea, but eventually accepted it as it allowed him to save Naruto from Code's onslaught in the Konoha woods. He did hate Amado's tinkering, but Kawaki ultimately knew that with Naruto and Sasuke both losing big parts of their arsenal, this mark would provide him power to protect them and the Hidden Leaf.
It was a sinister Catch-22 that also made Amado more valuable to Konoha -- no matter what happens, they'll need his expertise on Kawaki moving forward. However, given what Amado's sinister secret allows for Kawaki's body, his addiction to playing god like Orochimaru could spell doom for Boruto down the line.
Amado confessed to Delta that he alone knows about a failsafe he put on Kawaki. Thus, he can shut the kid down as a WMD if he goes berserker, which means Konoha would need the veteran scientist as a security measure if Kawaki did indeed break bad. But this behavior means Amado could also have messed with Naruto's son in the past.
When Momoshiki began possessing Boruto more, Amado offered some pills to help with Boruto's Karma mark -- meant to stop the Ōtsutsuki's alien DNA from taking over. However, the pills could have been Amado's way of slipping a failsafe inside the boy. Thus, if Naruto and Sasuke aren't at their best and Kawaki is also out of commission, Amado would be able to hold the Hidden Leaf's trump card hostage.
And if things got bad, he could de-power Boruto or maybe even kill him. It'd fit Amado's M.O. of using people, which was seen when he offered up the Jiraiya clone, Kashin Koji, as a pawn to Isshiki to drain the alien overlord.
-1.jpg?q=50&fit=crop&w=750&dpr=1.5)
Amado may even have hatched a nefarious plot to control the kid himself, which would allow him to hold Konoha hostage as Naruto would bicker with Sasuke and the other villages over killing his son. In short, it could stir up civil war if he made Boruto a puppet this way. In addition, if Amado has been messing with Boruto's mark but something backfires, that might allow Momoshiki to take over the boy's body permanently, giving the alien the ultimate form to use as a destroyer.
It's a very tangible risk because the scientist admitted in the past he doesn't know much about the Karma in the first place. It shapes a powder-keg, with even Eida realizing Amado was quite untrustworthy. It's why she's cynical over him taking her to Konoha to gain refuge. She can tell he's manipulating Kawaki, and given how he loves contingency plans, it's easy to see Amado using Boruto as a back-up too. Ultimately, it's in Amado's deceitful character and why Isshiki kept him close to the chest -- something Shikamaru and Co. may come to regret not doing.