At the end of Crysis 2 prophet is talking about how the ceph are all over the earth, not just New York and Lingshan. So why is Crysis 3 story line returning back to New York. Why aren't all the Ceph dead in New York, I thought the spore blast was suppose to kill them all in that radius.
What happened in the 20 year leap from CR2 to CR3? Did Prophet go all around the world and do the same thing at the end of Crysis 2 (lol) ?
Now to return to New York only to save a friend from the Cell Corporation, which only seeks world domination by controlling the Ceph (idk :| JK)?
-So many questions very few answers.
-Any answer would be appreciated.

I will post any good information here http://crysis3blog.blogspot.com/

The spore didn't kill all aliens purely because you can't kill everything, even nukes won't kill everyone will they? Prophet did not leave new York, as far as we know but it is unclear why he is still in new York, except that he is now on a journey of revenge to destroy cell (who have stuck bio-domes on new York to capture all the Aliens so they can steal their weapons and rule the world so that they can try and protect the human race) and to finish ff the aliens.

The 20 year gap bothers me. In 20 years the aliens would probably take over Earth.

Yeah I was hoping it would take place somewhere else, you know... feels as if all three games are going to be completely different story-wise :/

yeah the plot holes between 1 and 2 were massive. what M4dn3ss said, feels as if all 3 games are going to be completely different story-wise. even though we have psycho, it still seems to convulted.

Plot holes I can remember off the top of my head (SPOILER alert):
Crysis 1's cliffhanger ending was never solved
soooo did Nomad go after and find prophet eventually?
Prophet freaking shot himself, did he turn into alcatraz?
I thought crysis 2 implied that psycho died, yet here he is in 3
the whole aliens look drastically different thing
Where's the whole freezing everything and stuff?
so i guess alcatraz and nomad are dead, kinda stupid though
why is cell even going after nanosuit dudes, they give NO reason other than their commander hated alcatraz
whoever the phuck wrote crysis 2 storyline probably never even played crysis 1
and yeah, WHY NEW YORK again????

dunno if they can fix all those holes, it's possible but i doubt they will if they have the same gay storyline writer they had for crysis 2

Comic books explain what happened.

Prophet's mind is in the suit, so the suit is basically prophet.

Psycho left the island with prophet, so he could be alive, I guess they'll explain this in C3.

They adapt to the environment. Massive flying aliens aren't that effective in a place such as NY, with a lot of buildings and underground structures.

Well now, gotta agree with you there...
Uhhhh... Hargreave wanted the suit...

WIll people ever learn... same questions I've been answering in so many threads...
well as for why the 20 year gap question, Prophet (Alcatraz whose now calling himself Prophet) has been imprisoned by Cell right after the ending of C2 until C3. Pyscho was also imprisoned and could have been imprisoned since the end of C1, from all we know at this point in time. No, Prophet did NOT take over Alcatraz. (For more explanation on this, read just about any of the other threads I've posted in) Alcatraz just took on the name because he prefers it (according to the book).
Prophet (again Alcatraz... wish they didn't have Alcatraz change his name. Its confusing way too many people) returned to New York for unknown reasons, found the nanodome there and thought something was fishy about the whole Cell "protecting the civilians" thing.
How do I know all this? You might wanna take a look at my "Everything you need to know about Crysis 3" thread if you haven't already.

I think at the beginning of the trailer .. replied to this question

Yeah, but Hargreave is dead now...

He's now, he wasn't in Crysis 2.