Sabae thought that Kanderon and Alustin used her and her friends as bait for the demon Bakori, but it turns out that Bakori was not really considered a serious threat. Kanderon and Alustin admit they were wrong about that but they were actually busy preparing for a far worse threat. Given that hundreds of students and most of Skyhold's powerful council died to Bakori, that's saying something. No one knows why the ancient Ithos Empire that once conquered the entire continent suddenly fell apart hundreds of years ago. It fell because they killed the mate and children of a young sphinx named Kanderon who then used her crystal and planar affinities to create what she calls the Splinter, which exiled the capitol of Ithos to a far distant world. She knew it wouldn't last forever but hoped the population would die before the Splinter ran out of power and the city returned. There's no way of knowing when it will reappear, but more than one faction wants to be there when it does. An Empire that opposes the Great Powers like Kanderon wants both the Splinter as well as the Ithos weapon known as the Tongue-Eater. Unfortunately Ithos poses a far greater danger than those powerful items. Kanderon later learned of a race known as the Cold Minds, that devour whole worlds in an effort to escape death. When Ithos returns there is a good chance it will bring the Cold Minds with it, and they devour whole worlds.

Alustin and his four students are sent to scout the potential locations the city could appear while Kanderon and her allies prepare to take on either the people of Ithos, if they survived, or hold off the Cold Minds while people evacuate their world. Alustin has avoided mentioning his personal history to his students but with the Empire sending their elite kill teams after them he explains what Bakori meant by calling him The Last Loyal Son of the Bells and why he has fought the Empire his whole life. These kill teams are made up of five warlocks all pacted to magical weapons. While connected by the pact the weapons gradually gain sentience and the oldest of these weapons are well known such as Groveheart. Groveheart is a bow whose arrows sprout into trees on impact. This usually kills the target if it penetrates the body, or weighs down armor bearing mages like Godfrey. Finally many things about Alustin make sense as his students witness him battling for his life and using the full scope of his abilities. His students also come to realize that both Alustin and Audric, Godfrey's father, are not only Archmages but could claim the status of Lesser Powers if they wished. 

As they travel the four friends also discover that the world is far stranger than they realized. They visit Great Powers and even some of the eccentric Liches. Liches are powerful mages who escape death by investing decades and all of their power into a territory. Most build their territories into cities to attract residents since the final act of becoming a Lich means imbuing the territory with their spirit and magic so they can no longer travel and can only interact with the wider world through travelers. Liches also tend to be interested in pacting with Warlocks so Hugh learned about some of them while making a list of potential pact partners.

It is in fact a Lich who gives them their first solid evidence that Ithos is in fact returning as well as a warning regarding their destination. The Mage Eater is a tiger that hunts any mages who venture into its territory which gives them something else to worry about on top of warlock assassins and incorporeal world eaters. They may be the first group to reach the site once occupied by the City of Ithos but they are soon followed by others and the battle is on to defend the Splinter until Kanderon arrives to get it. Ithos is a dark and haunted place in it's exile and they are not alone.

The stakes keep getting bigger with each book in this series and the battles more astonishing. With The Lost City of Ithos the multi-world nature of the world building is greatly expanded. We learn that many of the Great Powers are not originally from this world and that some, like Kanderon, have traveled beyond it via the Labyrinths. There are factions out there that have mysterious goals on Hugh's world. At this point the series has left behind any impression that this is another "kids studying magic at an eccentric school" we got from the first book. Hugh and his friends are well on their way to being Archmages, which this world defines as not only powerful mages but mages who use their affinities in unique ways. They are also entering politics on not only their world but getting hints of the politics of their whole cosmos and starting to think about what they want to stand for.