I'm confused

Ok so in X3 Xavier says that Jean survived cause she was wrapped in a cuckoon. So why did X2 leave with a bird under water, was the original plan that she was gonna burst out the water, cause if she was in a cuckoon I don't get the phoenix under water bit at the end.

They changed directors. Originally they were going to use the fire bird, but it was cut out ((Which is one reason not alot of people liked it))

Also the fire bird at the end was basically to arouse interest that when X3 did come out it would be about the Phoenix saga. Then when X3 did come out is WAS about the Phoenix storyline so therefore that last shot fulfilled its purpose.

Maybe the Phoenix form underwater from X2 was her full power bursting free to save her, then it contracted and wrapped her in a cocoon to heal her and exert it's dominance.

This shud've been asked here:

X-Men 3 The Last Stand Discussion