I think the Alfar did it, but it was a faction within their government that framed them. If that were the case, it doesn't matter either way, because his objective of trying to prevent a war can't be accomplished while they see him as leverage at that point.
I also can't ignore the possibility they'd see the smartphone message as an Alfar trick and that the father would try to get him back.
I think the former is more likely though, unless the Templars have devolved so much that they just don't respect the Grandmaster any longer. The next few chapters are either going to have the MC leaving Alfar territory cutting his way through them to get away, or for him to refuse to leave out of principle and investigate in Neverwhere with Medb and them becoming an iconis duo trying to prevent a disaster.