How do you feel about the protagonist of a visual novel having his own motivation, possibly different and unknown (at least at the beginning of the story) to the player ?
It started so well, why did it had to end so badly ?
Unless you're using "protagonist" while thinking about one of the leading character (like by example the best friend that will do all the dirty works), the protagonist have to have his own motive(s)
and it/they have to be known by the player. This doesn't mean that everything have to be fully explained or plainly presented, but it must not be hidden.
Whatever how you'll write it, unless it's an not centered Kinetic Novel (in which case there's not really protagonists), the player will see the story through the eyes of the protagonist. It doesn't matter if the player self immerse or not, if the story is from a first or third point of view, or if there's scenes happening behind the protagonist back. The main part of the story will be presented to the player, and therefore perceived by him, like the protagonist perceive it. It would be a Multiple Personality Disorder move, with a protagonist not knowing himself what his own motives are.
Something most known as "what the fuck is this lame writing ? Dev's drunk or what ?" Because, whatever how effectively good you can be at writing, and whatever how seriously you crafted it, no writer can reveal mid story a protagonist hidden motive and looks like something else than a fool.
For it to feel natural and not seem to be the act of someone who absolutely don't know what he's doing, it needs hints dropped ahead of the revelation. And if there's hints dropped, then it's not different or unknown, it's mysterious.
It's not the same, especially since all the motives starts as mysterious. The player don't fully know the protagonist, and even protagonist don't full know himself.
"I'm helping her because I'm a nice guy" -> "Well to be honest, I'm helping her because I like her" -> "Okay, I'll be honest, I'm in love, it's why I help her".
There's no secret or unknown in that chain of events, nor is there contradiction ; he's helping her because he's a nice guy, that like her, to the point that he's in love with her. And it's possible that, when everything started, the protagonist himself wasn't aware of his real feelings for her.
But it's different with a chain of events that would goes like "I'm helping her because I'm a nice guy" -> "Of course I'm helping her because her parents are bad guys" -> "Gotcha ! I helped your daughter with not other intent than being able to avenge my parents that you killed years ago..."
A story can follow those tracks, but to be coherent (and therefore interesting), the player need to have strong enough hints regarding what happen. He need to know from the starts that the protagonist parents have been killed, and that he expect to avenge them soon or later. Like the story need to drop hints that the girl's parents aren't really clear, then that they are bad persons, then that they can possibly be responsible for the said killing.
Else, as I said above, not a single player will believe that you are something else that a really bad writer who absolutely don't know what he's doing.
Even a game as infamous, due to its way to numerous deus ex machina-like moves, as WVM, give us some hints. When, by example, MC's real mother save her son, running the car into his aggressors, we previously know that he's adopted, and we have suspicions that his real mother is possibly really near, keeping an eye on him or trying to enter in contact with him.
Her saving the day is a deus ex machina-like move, but her being near enough to intervene isn't much a surprise.
In a story, there should be no secrets, just mysteries that slowly unveil, through hints, in front of the reader/player.
A motive can be different than how it was initially presented, but the player must be in position to uncover this before the big reveal party, or at least to look back at what he know and see the hints he missed/misred.