If the three main churches in PL are torn down to build a church to Nerull, that is a repudiation of Pelor, Hieroneus and Kord. (As Elder Basilisk said) Who do you think the people will worship? The repudiated, powerless gods, or the god who saved them from plague, the one who is supported by the government and the military?
The loyalty of the military is already to the church of Nerull; making the agreement will only consolidate things. Good Nerullans will inevitably get promoted to positions of power in the army, and non-conformists will probably find themselves dead.
How the heck could Mortimer ever renege on the agreement? He won't be able to get the support of the 3 repudiated gods (in fact, he may need protection from their wrath), the allegiance of the people of PL will be to Nerull, and so will the loyalty of the army. The longer he waits, the more established the Nerullans will get. If Mortimer tries anything, the army will revolt, and PL too.
However, the Nerullans need not hold themselves strictly to the agreement. Some people will die, and disease will strike occasionally, but not at random. Disease and death will be explained as punishments for failing to respect Nerull and his clergy enough, or for consorting with heretics, etc., etc.. And who will notice when the frequency of these "punishments" starts to increase? A few wounded soldiers (devoted worshippers of Pelor or Hieroneus) happen to survive a lot less often than soldiers who venerate Nerull. Who's to know? The Nerullans will be perfectly placed to engage in a little bit of assassination, of blackmail, corruption, bullying; there will be the occasional "unfortunate incident"... but the people will be grateful for what good the Nerullans do, and be fearful of the consequences of not going along with the system, even if the system is gradually getting worse. The infractions will never be so blatant as to warrant tearing up the agreement, and will only consolidate the Nerullans more.
This might take time; 5 years, a generation, who knows? But the future will inevitably be a miserable one. And it will progressively sneak up on the characters. First as a fait accomplit, then as a system that gets more and more entrenched.
It's a poison pill, a bad deal. But does it make Mortimer evil? No. Naive and mistaken, certainly. In bad standing with the good gods. But evil? Not yet. He has to willingly throw in his lot with Nerull.
The next step might be by having the 3 good gods try to punish him; with the help of the Nerullans the curses and what not are lifted. In exchange, he just needs to participate in Nerullan ceremonies. Offer him magic items that are crafted by Nerullans. Normal ones at first, but stick in one every now and again that are a little bit edgy. And so on. Set him on a slippery slope towards perdition. Have him ok a suppression of an uprising that is motivated by anti-Nerull feelings. When he discovers that Pelorite clerics and paladins were executed in his name, what will he do?
Hopefully it will be to retire Mortimer and play a new character who will overthrow his corrupt and evil reign; and the Nerullans along with it!
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