1. When Missile got shot how come nobody heard? There's no way neighbours could not have heard that gunshot. Heck, if that lady next door was going berserk at Missile barking, how could she not have heard that loud, decisive, bang. She may be quite the character, but you can tell she's not stupid.

2. Can Sissel see people through telephone lines or not? So basically when Sissel gets back to the junkyard, he mentions to Ray that 'Lynne sounded distressed'. But at the start of the story when he was in the phone line for first time, he says that he SAW the face of the man that ordered him dead. So could he see what we saw, or not?

Why the hell the first time Missile died (10 years before) there was Yomiel with the hitman (at Lynne's house, when Missile gained Ghost Trick power), and 10 years later (after Missile waited the time to pass when he went back to Yomiel's death in the park), there's only the hitman when Missile is going to die again?

Yomiel had to act like he was dead after he made Lynne shoot him because a murder without a body would be quite weird.

So, the first time, he didn't made Lynne to shoot him and then he was there at Lynne's house with the hitman, 'cause he hadn't faked his death?

Oops, you're right! In that case, I have no clue why that happens, after all, the time lines only really split after Sissel decided not to save Lynne. That is a contradiction then.

Why did Sissel have Ghost powers at the end? He's in a new timeline now, where the meteorite didn't hurt anyone, so nobody should have Ghost Tricks.

Also, the black cat right there in the scene is Sissel. So, I don't think he should be getting any one of those ghost powers. Get it?

The meteorite went through Jowd's knee and "killed" Sissel. That's why he didn't age in those 10 years.

But, if Sissel is dead in the new timeline, why can he move his body? I don't think he can manipulate living beings...

If Lynne died her first death without Sissel doing anything, she would get ghost powers. Because she would die in the presence of Temsik radiation, emanating from YOMIEL'S BODY.

Yomiel could also move his body even though he was "killed" by the meteorite shard. Sissel's body is now cycling between life and death as well.

But he had the power to manipulate living beings, Sissel didn't!

I suppose the explanation that Lynne didn't get her powers after being shot the Nearsighted Jeego is simply because she was out of range. Remember Cabanela was shot at point blank range by Yomiel but didn't get any ghost powers.

From what I remember, Yomiel went to Lynne's apartment to retrieve the box with Alma's murder weapon inside. What I don't get is why he didn't go there in the timeline in which Sissel prevented Lynne's death. He was aware of Sissel saving Lynne throughout the game, so I guess that played a part, but it seems to be unexplained. Perhaps seeing Sissel use his ghost tricks to save Lynne ended up changing Yomiel's plans.
Edit: If that's the case, I wonder why Yomiel was aware of Sissel saving Lynne, but made no mention him saving Cabanela or the superintendent.

It's a pretty huge stretch to believe that Yomiel survived both getting pierced through the back and then having his legs crushed by the giant rock, completely without Temsik aid.

And lastly, Sissel at the end of the game is in the same position that Yomiel was. He was killed by the meteorite but now inhabits a body that never ages, since the fragment is still in him.

Cabanela said that he recognized the doctor as a fraud right away, and paid him off to take Yomiel's body away, which was why he wasn't in the apartment to give Missile his Ghost Tricks. The first time, I imagine he was too distraught about Lynne's death, and didn't notice anything, which was why the "doctor" could get away with the body.

And about that other thing, when Sissel saved Lynne, he wasn't very careful about hiding his presence, so Yomiel knew (since he knew about the Powers of the Dead). When you save Cabanela and the superintendent, you go out of your way to avoid him finding out about it, so it's likely he just didn't know about it.

There. How's that?