A plausible mechanic to "remove" a player character's weapons would be to force them into a VR simulation.
We saw similar to this with the VR pods in the Fallout games.
Putting a non-optional, unavoidable quest mechanic like that in the game, in my opinion, is annoying, and starting to get a little predictable and formulaic when it comes to games throwing that unavoidable device into the main story through interactive dreams, VR, jail, or some other excuse.
However, I find the same thing acceptable if it's done as a non-mandatory quest; something that's actually part of player decision making and a choice where any consequences and/or rewards, either immediate, or protracted and to be revealed later become meaningful because you made the choice to do that quest, and accept the results of the play through, even if the results are immediately detrimental to the character, instead of giving it a pass, and/or reloading to an earlier save.
I mentioned it earlier, and I think in another thread, perhaps the Story Line Suggestions thread, where V could make up with the Scav gang, and put them to work scavenging all the bodies V drops, but, maybe they still hold that grudge, and can they really be trusted, so, perhaps V gets lured into doing a milk run mission alone, and it turns out the Scavs, and/or someone else V gave a really bad day have teamed up, ambush V, and V wakes up on a table missing Arms, Legs, other parts, and is getting rescued by Jackie, or some other friend to come back full circle to that first mission where the "princess" needs rescuing, except now, it's V.
From there, you could have a big recovery montage, and a period of gimping by, somewhat nerf'd from your previous load out, calling in favors to get replacement limbs, and new gear, and now you're on a very personal hunt for some folks you might have tried giving a chance only to get back-stabbed.