The twisted fantasy plot is probably the oddest thing about Pandora's Tower. Elena is a needy little idiot with not much going on. Aeron is an emotionally awkward, gullible sadsack who barely speaks. Somehow these two people are in love and that drives Aeron to do some seriously strange things to stop Elena transforming into a sort of human slug.
Elena is cursed, you see, fated to morph slowly into a monstrosity should she fail to wolf down the raw chunks of beast flesh Aeron brings her. This flesh temporarily returns her to her human state, but to lift the curse fully she must eat the specialised meat of the master beasts (or bosses, if you want to be pragmatic) who reside in towers suspended over an eerie bottomless chasm. It's a boy-meets-girl love story with a Clive Barker twist.
Strange as the story sounds, it keeps Pandora's Tower rooted to one central conceit: the more time you spend away from the girl, the sicker and more beastly she becomes. Elena's health meter, which ticks down steadily as you explore each tower, is stamped permanently in the bottom left corner of the screen as a constant reminder of her deteriorating condition and an indicator of how much time you've got before you should really think about heading back and whacking another fillet of beast flesh into her chirping gob.
Occasionally, the game will cut back to show her pottering aimlessly around the house, falling over and sometimes just wistfully sighing the main character's name followed an ellipsis. A typical helpless Japanese videogame woman, then, albeit one who's found herself in a fairly atypical situation.
The flesh of regular enemies will delay her transformation long enough for you to head back into the tower and tear a chunk of meat from a master, meaning you can either try to speed-run these levels in order to grab the curse-reversing boss-meat or explore the tower more thoroughly (to find materials and new equipment) while making regular trips home to top her up with plain flesh.
Why can't you just leave a pile of beast flesh at home for her to nibble on while you're away, you ask? Because flesh dries out to uselessness once it leaves the tower, of course. There are no fridges in this weird world, sadly.
The transformation and subsequent scarfing down of flesh itself is rather harrowing. Spend a bit too much time adventuring and you'll find that when you return Elena will have slithered off into the basement leaving behind a trail of sticky, purple goo. In this state, her bubbling, blistered skin looks like molten blueberry pie as she, hiding in a corner and shrouded in shame, convulses and moans pitifully. It's grim stuff.
If you dote on her, however and regularly return to her before the curse really takes hold, the worst you'll have to witness is a bit of a manky arm. Either way, her protesting at having to eat these grotesque lumps of raw, dripping meat is the game's heartstrings-tugging, stomach-turning mainstay (and Pandora's Tower doesn't flinch in representing the grisly ordeal, either).
Her affinity for the protagonist will increase if you treat her well, visit her plenty and shower her in gifts, while ultimately your treatment of Elena will also determine which of the game's endings you'll see.
So that's the backstory and your ultimate responsibility. When you're not looking after your Tamagotchi girlfriend, the action plays out in hack and slash style as Aeron traverses each of the towers in turn, first discovering the location of the boss's room before destroying the giant chains that lock said room shut, running inside and ruining the day of that tower's master.