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The crawling chaos, Nyalathothep, has formed a cult on the mortal plane devoted to his cause which worships him as a god. This cult has been operating in secret for thousands of years, sowing destruction and chaos throughout humanity's history. He has sowed his taint into their genetics, providing a fruitful ground for many physical mutations among them. Considered gifts from their god, they have bred amongst themselves for generations, occasionally taking outsiders into their ranks to avoid inbreeding and becoming more corrupted and filled with his power. Now the time is ripe for Nyalathothep to enter the mortal realm, but for this, he needs a suitable host body, a perfect avatar, to contain his essence and allow him to walk the earth. This dark messiah would come to humanity as a living God and lead it to its next stage of evolution.

To be possessed by a god and being made one with him is considered the greatest of honors, one that all followers dream of being chosen as a host body. Unfortunately, none of his followers have proven suitable. Every vessel has rapidly broken down, unable to contain the essence of an elder god and forcing him back to his realm. What Nyalathothep needs is a human being lacking his genetic taint and unconnected with the cult. A being with a virgin template whose soul is uncorrupted and able to contain his essence.

However, this avatar would not simply be the elder god taking over a mortal body, but someone else entirely. The original host and nyalathotep will both cease to exist, their souls combining to create a completely new individual altogether. This being may have the memories of its 'parent' souls, but feels no connection to them personally.

How can you showcase a complete change in personality and ethics and do it well in a story?

There is a bunch of creative methods - some more than other - that can help you.

Here are my ideas:

Change the narration style

One of the most clear ways to signal that something has changed is making changes to the narrator.

It's a pretty solid and, well, obvious advice if you have a first person PoV on the characters who changes: having direct access to his/her brain will make your job easy. Your pretty average Joe/Jane can become an alien, elder god reincarnated in the following chapter. Nobody expects his/her thought process to be the same.

This approach, thought, could be done even if you are using other PoVs. For example, in third person limited you could still portray the alien thoughs of the newborn character with a clear difference in themes, patterns and voice.

Radically change the narration style

While the previous point can be done in a kinda subtler way, nothing keeps you from doing something more daring on a meta-literature level. For example, you could change the PoV entirely:

Chapter X, 1st person pov Joe:

... I felt blood pouring from my eyes in hot trails of tears, then my headache exploded until I couldn't feel anymore.

Chapter XI, 3rd person pov Newborn elder god:

The thing awakened and realized it was alive. That idea painted its face (human, and rather ugly for its standards) with a rather quizzical look. It stretched its pale, sleek finger-appendices around as it tried to got use to its body.
The thing sneered. It didn't like how the memories from its parents mixed and tainted one another, even if - admittedly - the knowledge of one vastly surpassed the other.

Kick the dog

In telefilms, "kicking/petting the dog" is a trope where a character is showed doing an act generally considered evil/good. After the change, you can have this kind of "ethically loaded" scene where your character acts different than expected.

Whatever was the moral alignment of the human character, I suppose the newborn elder god will have a wildly different sense of ethics, so there is a lot you can do to show the change. Forgive me if I recycle an old, nasty piece of black humor in the next example:

The woman waved to it, unaware of its recent new birth.

"Hey Josh. By any chance, I was wondering if you could help me buy some groceries for the homeless canteen, like we did last month."

"GROCERIES" the thing noted. "WHY THAT?"

"W-well," she answered "we need to have something to cook for them!"

"I SEE. I SUPPOSED WE WERE FEEDING HOMELESS TO THE HOMELESS."

Of course you could play this in a number of ways, depending on how you want the new character to be like. This brings us to the next point:

Alter character relationship

If the character changes, all its connection with the other character will change as well. One good way of making the audience notice is making the other characters notice. Anyone who knew the old human guy will notice changes in his/hers behaviour, exspecially if they were close. I'd rather say that the closer they were, the more evident the changes will be.

All for now, even if I may come up with a later edit.