I ... would not recommend that, if only because of the long-term game issues. Why not have several different AI, each believing themselves to be Deus recompiled (and the others enemies/blasphemers/however you want to put it), try to take the place over? That way the majority of the tussle is between the various AI, and the PCs can move between the monoliths the way shadowrunners are meant to, gearing up to take each one down - or all of them down simultaneously. Because if it's actually Deus recompiled, you have it spreading through the hub in nanoseconds, seizing ownership of everything electronic, spotting anything it cares to look for (presuming it's in range of a network-enabled camera) in a matter of a few seconds, a minute at most, and walking out to take over the world in a matter of days, because the digital cordon would go down whenever Deus wanted it to - just like the Arcology.
Understand that if recompiled into the SR5 Matrix, Deus has innate, instinctive, and complete connection to the Foundation, and knows it. This is a part of being one of the Big 3, all of whom could (we know 2 did, and Morgan/Megaera might have as well) create otaku and establish resonance effects. So the typical 'AIs can't reach into the Resonance Realms' bit wouldn't work for Deus, because he's a part of them - theoretically, anyhow.
Without anything on his level to oppose him (i.e. either of the other two Big AI), he owns however much of the Matrix he wants at that moment.