and the image didn't pleased him at all.
Please
His dull black hair was being too rebellious that to be combed properly, and his face featured a pair of beautifully dark eye bags of a very curious purplish color, a proof of the little sleep he had had the night before.
There's a bit too much going on here. I'd advise simplifying it and maybe splitting it up into two sentences.
"His dull black hair rebelled against any attempt to comb it properly. Plum-purple bags under his eyes reminded him of how little sleep he'd had."
An unsettling thought appeared in his mind that night half a week ago, and it stubbornly stayed there, forcing him to doubt everything he saw, heard and knew.
Tenses are a bit weird, especially since you don't establish that this is talking about the past until halfway through the sentence. I would rearrange it into something like.
"A thought had been stuck in his mind since that night half a week ago, refusing to leave, forcing him to doubt everything he saw, heard, and knew."
For his sense of what is real and what is not had been crushed by the truth.
You could say the same thing more efficiently as "His sense of reality had been crushed by the truth."
From his window he could see how the sun slowly started to hide behind the tallest buildings of the city.
"from his window he could see the sun slowly starting to hide behind the tallest buildings of the city"
Again, strive for efficiency of language. Don't use two words when one will do.
his doubt was fighting with tooth and nails to make him change his mind.
I think the way this is normally used it would be "his doubt was fighting tooth and nail"
His gaze unconsciously drifted toward the ancient and thick hard-covered book lying on his desk, the golden letters of its cover, shining with the reflected light of twilight, read: "The Book of Eleven Hours: Tome I".
Again, a bit too flowery with the adverbs/adjectives. This could probably also be split into two.
"His gaze drifted toward the hard-covered tome lying on his desk. The golden letters of its cover, reflecting the evening light, read: "The Book of Eleven Hours: Tome I".
(I also think titles are formatted with italics, not quotes? Not 100% sure though)
How he and Emma were arguing over some silly triviality, and then they foolishly allowed the fight to escalate beyond control, she said horrible things and he replied with worse ones until… it happened.
"He and Emma arguing over some triviality, the fight escalating beyond their control, the horrible things she said and the worse ones he replied with until… it happened."
he love her with every fiber of his being.
"he loved her"
They had met for first time in the science history museum, at the main street, and after a little chat and shared chuckles Joe realized she was perfect. Attractive, clever and funny. She was so full of knowledge about long dead civilizations and religions. She had the same interests in literature and ancient myths as him.
This could be expanded. Show us a bit more, go into a bit more detail, rather than just quick descriptions. You've got as much space as you need, so feel free to use it.
Except not quite. She was also a bit too much involved with the occult. Joe always found intriguing the rituals and beliefs of the old times, but for Emma it was an obsession. She was passionate about it. She believed in legends and fairy tales.
Again, a bit more tell-y than it should be. Give us examples, situations, reasons to believe this other than "one sentence said so".
For Joe it wasn't much of a trouble. Even if he was open minded, he was skeptical about the idea of spirits and monsters and magic. For him they were just very entertaining stories, not deeper than a novel or a children's book. He liked to think he was a man of science, after all.
see above. I could see all these bits working as their own, seperate flashback chapter. It's generally not good to start a story out with this much exposition.
