To start with, note that Pandora's Tower revolves around romantic love. The main characters are Aeron, the male player character, and the female lover Elena that he ventures out to save. The fact that you have to keep coming back from the towers to take care of her - she's transforming into a monster because of a curse and needs to be supplied with a diet of perishable monster flesh to retain her humanity - is compared to a working husband coming home to see his wife in the Iwata Asks interview. In line with this, the game also heavily draws off of Chinese alchemy and Taoism, as a central principle in Taoism that there is a masculine aspect (yin - the white part) and a feminine aspect (yang - the dark part) and rather than either being good or evil, we need a balance of both of them (e.g. that's how we get babies).
The most explicit example of this is that there is literally a boss in the game that is a monster yinyang. Take a look at the Masters of the Blacklight Barbican. Notice that the white one is masculine and the black one is feminine, albeit in a very beauty-and-the-beast way. They're also the second to last boss of the game, giving them special prestige.
So, now having established the general theme, let's get int the actual game world. Admittedly it's been a while since I played it so it's possible that I've gotten details wrong, but I think I remember the gist.
There are several countries outlined in Pandora's Tower, and some of their belief systems are alluded to, but the primary country is Elena's homeland of Elyria. A few of their religious beliefs are outlined throughout the game. One is that they're vegetarians, which makes eating the flesh of monsters particularly disgusting for Elena. The other is that they're polytheistic. Their gods and goddesses mostly line up with the Chinese alchemical elements - fire, water, wood, metal, and earth - with a god encompassing the male light aspect and a goddess representing the female dark aspect for each. There's also a more general pair in the god of light and goddess of darkess.
(The player character Aeron, for the record, was a soldier from another, more industrialized country that fought against Elyria in a war.)
There are three historical periods which are important to the towers that the game revolves around. Aeron and Elena's visit is the latest one, and the others are seen in flashbacks and read about in leftover texts. The Kingdom of Elyria plays heavily into all of them.
In the first period, the Elyrian people are left suffering while they participate in a long war to unite the various countries of the continent. In their distress, the people begin looking for new spiritual answers and develop an interest in monotheism. In order to facilitate this and calm the people, religious leaders in Elyria come up with a plan to switch to monotheism by
combining their actual gods together.
The thirteen towers, then, are built for this purpose. Originally they're even referred to as temples. The Elyrians enlist the help of the mystic Vestra people, agreeing to grant them their own homeland in exchange for their service. This process has them create the Masters, beings that represent the power of a particular god. Each was created from a single person. Their powers would all be combined together into a new unified god who would instead be created from a man and a woman together.
The pair that volunteer was a married couple whose son had been trampled during the war. However, unbeknownst to anyone, the two had conceived another child shortly before the experiment. It was discovered when the experiment was underway, as the presence of the third person caused it to go awry. The husband and child were saved. The wife was not. She was left as the final, incomplete god, Zeron.
With this failure, the towers were abandoned and sealed by the Vestra. The husband left and raised the child on his own.
The second period happens during another war around five hundred years later, this time as countries fight to liberate themselves from the union brought on by the previous war.
The towers are unsealed and revisited by the Elysians. However, rather than having a religious purpose, it's now the Elysian military that reopens it. They find the towers to be extremely interesting for a variety of purposes. They're resource-rich, magically creating an everlasting supply of rare and useful materials. Researchers explored the tower, filling it with notes on their various findings. There are even patent applications filed.
However, what they're particularly interested in are the Masters, the beings in which their predecessors has installed godly power. The Elyrian military viewed their power as an incredible potential wartime asset and created a new set of Masters. They also created a variety of lesser monsters.
They finally set their eyes on completing the goal that their predecessors failed to do and create the final Master. Deciding to do it without the Vestra, this ended up being an even more fantastic failure than the last. The Masters were not combined, but the world suffered from severe natural disasters resulting in large numbers of fatalities. It tears open a chasm - the Scar - under the towers from which monsters flow, and which gradually widens.
The towers are resealed, which also keeps the Scar from widening and eventually destroying the world. The military abandons it once again, leaving the Masters and the monsters to overrun them.
A few decades later, Aeron participates in the war against the Elyrian army just before it ends. There he meets Elena and they become lovers. In a festival afterward, Elena is struck with a curse. This leads to the events of the game and the final period of activity in the towers.
Aeron heads into the tower under the guidance of a Vestra woman, Mavda, so that he can use the flesh of the Masters within to stave off and eventually end the curse. He slays them one by one. But when all of the Masters are dead, Elena is not cured. Instead she is transformed into the revived Zeron - the final boss of the game.
As it turns out, there was nothing special about Elena. Rather, she was targeted by the curse because she was Aeron's lover. Aeron is a descendant of the child born during the experiment that created Zeron, and in her eternal grief, she associates him with her husband and the broken promise to be together that they had made hundreds of years ago.
So, to bring us back to the question that's the subject of the thread. Zeron's the final boss that you have to defeat. She's the one that sets the plot of the game off. She's the one you have to destroy to end the game. But is she the villain of the story? I'd actually say that the villain is Elyria itself; the history of atrocities carried out by its leadership and its military. Zeron is simply a notable victim, partly of bad luck.
This is evident in some of the games multiple endings. In one of the worst endings - almost all of them are tragic or bittersweet - the curse isn't lifted. Before that can happen, the Elyrian army returns to the tower and raids Aeron and Elena's hideout. They capture Elena and employ her as a weapon with which they can subjugate other nations. She's still together with Aeron, however, who is brought into the Elysian army.
As for the best ending, the main reasons it's the best ending - and kind of out of tone for the game, frankly - is that Elysia's historical crimes become known and work is put in to address them. It also ends up splitting the continent into several countries again in the process.
