Let's build an alternate timeline where Avernum is wiped out!
Avernum 1 - Nothing changes. Hawthorne and Pyrog die.
Between games, the Empire launches the Avernum invasion, and steals the Crystal Souls. In response the barriers go up.
Avernum 2 - The "War Heros" are summoned to take a treacherous journey down some insanely dangerous rapids. Predictably, their boat is smashed and they drown. Formello in desperation even sends another group down (Warrior NPC who was able to join party in past, temple priest, library wizard...). They also die in much the same fashion but I feel it's important to give a couple failed chances at the journey. It's established in game that if you don't bring down the barriers (By refusing to let the Oglai Council search your mind), the Empire figures it out first and Avernum is carved up piecemeal and destroyed. This is where the new timeline begins.
Avernum was slaughtered, maybe a few holdouts managed to hide from the massacre such as in the Honeycomb, but they wouldn't last long and likely would be of no consequence. Just for fun, they were even able to finish their massive portal.
The Empire now has two options: Join their Vahnatai helpers in their civil war (Their allies wanted to bring an end to Crystal Soul worship), or leave the savages to kill each other. I think they would leave, leaving behind their modified giants and demons to wreak havoc with anyone foolish enough to try to rebuild Avernum. Garzahd is still alive, and he has control of two dragons (Khoth, Sulfras) since Sulfras described being shackled as Garzahd taking their mind. Mortrax is dead, so they'll carry out similar experiments on his corpse as they did for Pyrog. Athrons fate is debatable, since everyone knew she exists, but it might well not be worth the Empire's trouble to go after her. So Garzahd withdraws with two live dragons and three crystal souls to play with. The Oglai Vahnatai launch a desperate attack on Ornotho Ziggurat that fails to even recover one Crystal Soul. During the ensuing Vahnatai civil war, the Oglai Vahnatai keep awakening more warriors and they will win out over their rebels eventually. Now Rentar gets to work on the plagues.
Avernum 3 - Valorim is utterly devastated, but the core of the Empire is undamaged.
The Slimes burn much of Kriszan, but eventually are stopped whenever Garzahd bothers looking for the source. Throw a bunch of fireballs at it, it ends.
The Isle of Bigail essentially winds up getting the "Nuke it from orbit" treatment to wipe out the roaches. No need to find the filthy factory itself, it simply burns along with the rest of the island.
Troglos and Giants can be solved by simple force of arms, something the Empire can eventually bring out, especially once we consider the golems.
The Golem factory is the real fun one. Garzahd has been researching on three crystal souls for years now. All it takes to find the Golem factory is some flying around(Drake Lord, Wizard). I think he would be able to take it over using his research on the Crystal Souls. So now Garzahd has taken over an army of golems and can launch an assault on Footracer province.
Alien Beasts are taken out by the full might of the Empire's Army that they couldn't use during the Avernum War, in addition to an army of golems. The assault then continues on to Rentar's keep. Rentar retreats into the deeper caves. The Empire does not forget and looks at another invasion of the underworld to deal with the latest threat.
Next up we can look at the second trilogy, so spoilers for people who haven't played those yet:
Avernum 4 - Rentar rebuilds similar plagues, only attacking the surface again. Losses are inflicted, but this time the Empire was ready and they are minimized. Meanwhile, the Empire was preparing to launch an invasion of the Vahnatai lands, so they do. They've had decades to build a teleporter network to move massive amounts of troops to the underworld, not to mention the one left over from the previous war. They take heavy losses, but Rentar falls. Quite frankly, the second plagues from Rentar just don't seem anywhere near as dangerous as the first wave given the amount of time to prepare the second time around. A few years led to an army of golems and the alien beasts. A few decades gives us three shades and krakens. Rentar also had a lot less supporters the second time around though.
Avernum 5 - Because Garzahd didn't die, the Empire doesn't soften up, so the Darkside Loyalists never happen. The Empire's power is not diminished at all. If Athron lived, Melanchion is pretty lonely without all his followers. He seeks out the deep cavern Sliths. More Vahnatai wake up to find a genocidal army attacking them. They're not ready for this and are slaughtered.
Avernum 6 - Deep cave Sliths and Melanchion find the caves being populated mostly by The Empire's army bent on wiping out all life in the underworld because they've been attacked three times by the underworlders now (Hawthorne, Vahnatai x2). Even if the Vahnatai and Sliths allied, which they won't based off what the Vahantai say about them, I can't see them winning. Prazac is dead of old age at this point, but Garzahd is still around as mostly a Lich at this point (Solberg, Patrick getting to decide when their time is up as opposed to old age). Garzahd can pretty much create Golem Factories wherever now, and the Vahnatai happen to have a whole bunch of conveniently located Crystal Souls to run them for him to avoid the problems Solberg had with a large number of Golems. Gladwell and Melanchion are pretty much non-factors if they're even alive. Not to mention the Empire is well established as Dragon killers and able to defeat powerful mages (They were able to send a whole pile of them to Avernum at the same time, including Erika).