No one mentioned it, so I guess I'm gonna throw it under the bus. Indigo Prophecy.
The entire game is one big plothole. I've played it, and actually, this is the only time I felt compelled to disagree with Yahtzee over a game in that I don't mind the QTE's, but a storyline that just kinda throws its hands up in the air halfway through and says 'I got nothin'; but here, take this lovely pile of poo my dog laid in your yard this morning...' really kinda gets my goat.
Okay, so we find out in the beginning of the game that Lucas has seizures (as you find the medicine bottle for them) but THAT just seems to go nowhere except to say he's a character with epilepsy.
You can have a variety of interactions with your estranged brother; but given what they went through together growing up; they never get around to why they drifted apart so badly as to not even talk to each other as adults. And why he doubts everything Lucas tells him? Strictly speaking as an Agnostic; if you're going to believe in a mythical all-knowing invisible being, why not believe what your brother is trying to tell you? Just throwing that out there.
It's obvious that Lucas dies very shortly after his girlfriend is killed. Aaannnnddd THIS is pretty much the point where I stop playing the game any further. I enjoy it to this part, come up with my own ending, and start over again. What conspires afterwards doesn't makes sense without the help of a few dozen drops of acid. We have a very confusing cutscene of Lucas and his brother as children, then later on the storyline is highjacked by 'The Cultists' from the Silent Hill series, who believe in some 'insert generic ancient civilization god here' type deal. And the entire fate of the world depends upon a little girl whom five seconds before this took place, you didn't even know existed in the game. Lucas randomly comes across the woman who throughout the entire game has been trying to bring him to justice/kill him, et al; but within hours of them meeting, she ends up not only sleeping with him, but 'falling in love' with him. Can everyone say 'WTF!?' with me?
The game starts out great, and there are scenes that are truly inspired. But the whole thing falls apart after Lucas and his girlfriend die. Oh yeah, speaking of her, this shouldn't surprise anyone, but she's never mentioned again. There's no mourning, nothing.
Yeah, I guess I could mention that the entire planet has gone into the next ice age and the only person who can stop it is YOU, with your unknown-before-now powers that you just pull out of your ass now that you're DEAD.
It's been a few years since I've played this, maybe I'll play it again just so I can remember clearly all the other plotholes that pissed me off.