Ok so the cult brainwashed Walter to commit the 21 sacraments saying it would resurrect his mom when really it would resurrect god.

Well why don't they just do it themselves, they're a fanatical cult i'm sure this is something they would want to do rather than banking on some random kid actually deciding to do it (very unlikely), then actually being able to follow through on such an incredibly difficult task.

Furthermore, since Walter read the scriptures and was taught in the cult's teachings, wouldn't it be obvious that the scriptures where talking about god being resurrected by the ritual and not his mom?

And how where they able to convince him that the room was his mother?

And also why was it that he was able to sacrifice himself in the back room without it smelling, and if he killed himself in prison why is he in the back room? And why did he have to sacrifice himself there specifically?

The cult didn't specifically brainwash Walter to force him into resurrecting any god. They may have singled him out as an exceptional kid at Wish House, but I don't think it extends beyond that. Even though the cult has a bizarre belief system, they're like any organised religion in that the majority are mostly interested in either spreading their influence or maintaining the status quo. With the exception of Dahlia's group, all of the resurrection attempts in the series have been performed by extremists for personal reasons.

The story is about a kid who was abandoned, and experienced abuse and religious indoctrination through the system he ended up in, which contributed to developing an abnormal psychology. He became fixated on his birthplace and his missing mother, and made the correlation between a particular scripture and his own mother figure; this is not an association most cult members would make, it was Walter's warped worldview alone. If the cult were in on it, they probably wouldn't have allowed Walter to murder prominent cult members such as Jimmy Stone.

I think it was hinted at in the game that he somehow faked his death in prison, or that someone else was convicted as him, but given his later supernatural abilities it's not out of the realm of possibility that he did kill himself, came back from the dead and sealed himself in the back of room 302. It looked like he used plenty of chemical preservatives to keep his body from decomposing, which would account for the lack of rot. As for why he did that in the first place, looking at the apartment as sort of a metaphorical womb, it would make sense to him that the strongest connection to the mother he was trying to resurrect would be there.

Another factor is that the Conjurer of the 21 Sacraments might need to be gifted with special powers, like the Mother of God. Walter is specifically compared to her in a text file somewhere in the forest area.

I'm positive that this is answered somewhere on SHH; but since this thread is started I'd like to ask something I don't understand...
Why does Walter's body look different in the hidden room that Henry finds compared to how Walter looks everywhere else?

^Because the Walter we see in the back room of the apartment is his corpse from after he performed the ritual of holy assumption on himself. The Walter that chases us around is basically a ghost Walter existing in Walter's otherworld.

Walter's story can be a bit confusing. I'd recommend checking out the SH4 section's Quicklink thread for guidance on reading more about him.

The "crucified" Walter in the back of Henry's room is the real Walter. How he looked when he was alive. And the one we see chasing Henry in the Otherworld is his soul.

I spoke about it before, it's almost as if he became a dark Buddha after the ritual. Assumption pretty much means "ascension". His light colored hair could be a nod towards it, I don't know.

Just to clarify, it was Dahlia who told Walter about Room 302 being his mother.

And if I'm not forgetting things, the Walter in the back of the room is the real Walter who killed himself in prison. It was Ghost Walter who dug him up and crucified him for the Holy Assumption.

idk

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Ok so the cult brainwashed Walter to commit the 21 sacraments saying it would resurrect his mom when really it would resurrect god.

Well why don't they just do it themselves, they're a fanatical cult i'm sure this is something they would want to do rather than banking on some random kid actually deciding to do it (very unlikely), then actually being able to follow through on such an incredibly difficult task.
^
Walter wasn't just some "random kid" that they picked. They chose him because he specifically yearned to see his Mother, and figured "Hey, let's use his yearning for his mother, to birth The Descent of the Holy Mother (god).
Simple, psychological manipulation.

Furthermore, since Walter read the scriptures and was taught in the cult's teachings, wouldn't it be obvious that the scriptures where talking about god being resurrected by the ritual and not his mom?
^
Dahlia told Walter that the teachings would help Walter see his mother again. She never told him about them birthing god. If she did that, it would raise an eyebrow.


And how where they able to convince him that the room was his mother?
^
Like this:

"Walter, your Mother resides in Ashfield, in the South Ashfield Heights apartment building. She is waiting for you in Room 302."

Dahlia said something like this to him anyway, it is in Walter's diary, I believe Eileen reads them on the rocks in the Forest World.

And also why was it that he was able to sacrifice himself in the back room without it smelling, and if he killed himself in prison why is he in the back room? And why did he have to sacrifice himself there specifically?
^
The storage room where his corpse is DOES smell. Watch the cutscene when Henry breaks the wall to get inside. His reaction signifies that it stinks pretty badly.
I personally theorize that Walter Sullivan DID kill himself in prison, it wasn't someone else, like what Joseph Schreiber thought.
Because Valtiel was "snuck into Walter's mind", Walter was able to be reborn as a "ghost/spirit", and then dug up his physical body, corpse, and took it to Room 302, where he did the Ritual of the Holy Assumption.

He chose to sacrifice himself there probably for privacy reasons. ( usually when people do rituals/meditations, it is done in a quiet, isloated area, for concentration and also to avoid any outside interruptions).