The boy is a benign tumor, sneaking his way unnoticed through the host. The game world is the human being itself. The men in what appear to be white masks are indeed white blood cells, looking to destroy or contain foreign material in the body. I don't have a good grasp of human biology, but I would guess that the dogs and humans each represent different facets of the immune system.
This tumor is causing mild issues with the the victim, prompting diagnostic attempts to locate it. In the game, these are the spotlights. If found, the tumor is excised, represented by the spring loaded harpoon.
The tumor is difficult to spot, however, and the immune system has trouble differentiating it from normal bodily processes (the conga line scene.) The tumor eventually interacts with these normal bodily processes (controllable zombie guys), even using these otherwise dumb processes to its own advantage, growing stronger and more destructive (the various sections where you control the zombies.) I believe the rows of these mindless zombies walking are meant to evoke blood flowing or other fluid movement.
As the tumor reaks more and more havoc, chemotherapy is attempted. In the game, we are talking about the water-hair-things. This aggressive treatment can be quite effective in targeting cancer, but comes with it great risks. Indeed, later, we see many otherwise useful bodily processes have been isolated by the immune system (upside captured zombies) due to having been corrupted by the patient's harrowing medical treatment.
Eventually, radiation is used (the "air blast" sequence) which seems to be destructive on the body but effective on the tumor. If the tumor survives this, we are looking at the doctors pulling out all the stops: more surgery, more chemo. Eventually they are successful, and the tumor stops it's reign of terror. This is when the long hair creature pulls you to the depths.
However, like many cancers, our hero goes into remussion for a time and then comes back even more dangerous (rebirth with the water breathing ability.) It ultimately makes it to another cancerous mass that seems to have been successfully contained (the Blob), takes control, and now we have a full bore malignant tumor on our hands, causing untold destruction as it runs amok.
In ending one, I believe what happens is that although the patient suffers greatly, the tumor is eventually removed and dies (lying outside the body on the shore, immobile.)
In ending two, where you play that secret song and find the other room beneath the cornfield, this is a scenario where the still undetected tumor attacks something vital, killing the host rapidly (lights out after you damage the apparatus is the secret room), which of course leads to its own death.
La paternidad lo cambia a uno mucho. Demasiado.
