Of the four conclusions, there is no one correct interpretation. Each ending indicates a different possibility.

in water
He came to this town to take his own life in a place of memories

James lifts Mary's lifeless body in his arms and leaves the sickroom. His destination is...
After the violent sound of brakes, a view from beneath the surface of the water fades in. Finally, the screen fades to total darkness.
He leaves this town as a man who has accepted reality

As James expresses his anguish, his wife lies on the bed and imparts her final words to him.
James makes his way through the cemetery where he met Angela and leaves the town with Laura.
A man who has murdered his wife a second time continues to live immersed in a delusion

In the case of this ending only, not Maria but Mary waits on the rooftop of the hotel. She vehemently blames James for killing her.
James makes the decision to continue to depend on Maria, the product of his delusion.
Leaving the town from the observation deck that is the starting point of the story. Could this suggest that nothing has been resolved at all?
To resurrect his wife, he carries out a forbidden ritual

The four special items all have to do with Silent Hill's long-standing religious tradition.  This reveals a point of contact with the preceding work.   
James rejects even the fantasy that he himself has created to escape. That unadulterated emotion is...
Finally, James is driven to carry out the forbidden ritual that can bring the dead back to life.

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