As co-author and co-plot developer of Pantheon, here is how I see it.
Importantly, the Pantheon temple is situated on a post-Apocalyptic earth that has been scoured, not just of humans, but of all life. This setting inverts and subverts the reigning paradigm of secularism, in which God (and all Gods) are dead. Instead the Gods abide and humans are dead. The source of this apocalypse is never indicated, but one is free to infer that it is a dramatized indictment of human stupidity and corruption in slowly destroying the planet through global warming, resource depletion, overpopulation, etc. Or maybe humans perished because they abandoned God worship. So instead of people and no Gods as we have today, in the far future we have Gods with no people -- though the rest of the cosmos remains populated with other, alien mortals, who perceive the Gods and their artifacts of worship through the lens of their own particular perceptual, cognitive and emotional structure.
For me, a theme is: Did mortals invent the Gods, or did Gods invent the mortals? Or do both invent each other? Or are they independent of each other? The fact that there are no longer any humans extant cannot cause the Gods to disappear, for as mentioned, there are other mortals on other worlds, like the Wheeled Ones. And there is one remaining human mortal: the immortal mortal, Cartaphilus, who as it develops is the Wandering Jew, condemned by Christ to wander the earth "until the last day," but the last day never comes, for in the far future as now, Jesus obdurately refuses to reappear and instigate the End Times: It is like waiting for Godot.
These Gods are powerful but not all powerful; they are a throwback to the days before the Abrahamic monotheistic God. And though they cannot die, they can manifestly suffer. There are many Pantheons, but the focus of the story, the Pantheon, is a group of Gods dedicated to subverting God worship: they want to confiscate the artifacts of worship that still litter the cosmos where (non-human) mortals still dwell, to destroy God worship. It is, however, somewhat ambiguous why they are on this mission; less ambiguous is why their founder, Cartaphilus, is on this mission: as it develops in the course of the narrative, he wants not just to destroy God worship, but destroy all the Gods and everything else, including the Cosmos. He is terrified of his own immortality, by which, like the Gods, he lives forever; but unlike them, he lacks any special powers apart from his considerable cunning and intelligence. He has come, monomaniacally, to plot and strive (in secret) to wipe out everything, himself included, if this is possible. Yet it also develops that he is afraid to die.
In addition to the Gods there are also the Undergods (3 fates) and utterly inscrutable Overgods, exemplified by a mysterious Golem who yells DADA! at one point to break up everything. Then there is the former Pantheon member Jalamdhara, who schemes in secret to re-introduce sentient life to earth and make himself their sole object of worship; and Chaos, with his eight-pointed Star, who just wants to fuck everything up for the pure hell of it, somewhat like the Joker in Batman.
Add to this brew the impetuous and captivating Kaeli, who is trying to recover her memories of her distant Godhood past, and all the other Pantheon Gods with flaws and neurosis and obsessions of their own -- such as Thumos, strong enough to hold up the whole Cosmos, as he does at one point in the text, but not strong enough to overcome his unease over being esteemed primarily for his muscle and not his mind -- and seeds of drama are introduced, to flower into manic cataclysms. The Gods are condemned not just to live, but to live forever: what could be more existentially boring than that?