The Anti-Christ in the Name of the Rose

When he says that, he doesn't really speak of some actual supernatural incarnation of the antichrist, but of the antichrist that could be said to symbolically stand behind every factual and concrete evil action of humanity. What he actually says is that the ignorance and evil of men has won yet again. It is a bit of a wordplay supposing the concrete meaning of the antichrist, as upheld by the Inquisition and others in the abbey, with a rather metaphorical meaning of it as merely a symbol for a hidden malice behind all actions that ultimately tries to produce evil in the world

While there were people among the abbey, in particular the ultimate perpetrator Jorge de Burgos and Inquisitor Bernardo Gui, who claimed those deeds to actually be supernatural actions of the antichrist, William suspected a real human murderer behind everything and he was right. But you could argue that the antichrist could as well be seen in a more symbolic way as the ultimate evil force behind all the actions that lead to the demise of the abbey. And this doesn't just include the murders but also the ruthless deeds of the Inquisition that let the wrong people burn in their fanatic fervour and worked their way against a rational investigation of the case.

In fact this meaning is also alluded to by William earlier when he, not without satire, says

The only evidence I see of the antichrist here is everyone's desire to see him at work.

So at this point when Adso says that after the Inquisition decided its verdict on the supposedly innocent convicts, he is playing with that notion of the antichrist, introduced to the story earlier in a much more concrete way, now using it in a rather metaphorical way (and maybe also a bit as a paraphrase of the real human perpetrator behind all those supposedly antichrist-facilitated actions). He alludes to the fact that everyone involved in the situation believed to act in their best faith, but against everyone's best efforts the whole investigation in the abbey resulted in the worst of all outcomes.¹ So you could say that the antichrist yet again won, even if he did not really need to appear in a concrete form at all.

1) _{In fact this contrast between trying to act in best faith and still producing the worst outcome is also alluded to in Umberto Eco's base novel when Adson, in his form as the actual narrator writes about the final chapter}

_{In which the ecpyrosis takes place, and because of excess virtue the forces of hell prevail.}