Mother is a series that stands out from other RPG most notably because of its silly and bizarre setting and humor. Mother is also recognized by its disturbing and even heart wrenching twists that go almost entirely unexpected. These twists firmly root themselves in the player's mind. You ask someone what they remember from the games, and these twists will most likely be the things that come up. These twists are where I've pulled some idea from. I don't particularly care if these ideas are ever used or not, I just want to get it out there for others to see, and perhaps pull inspiration from.

Following this opening is a potential boss idea, optional or otherwise, plus some plot work-ins to help prevent it from seeming too much like a Giant Space Flea From out of Nowhere, even though it kinda is.

Throughout the game, the main characters may come across a young girl, quite ordinary, although with a unique sprite to ensure she at least stands out somewhat in the player's mind. She may show up in several locations (Most likely towns) as a simple wandering NPC as the game is progressed. When spoken to, she'll seem generally reserved and distant at first, giving off the air of deep inner turmoil. She'll show a general indifference to plot events, seeming rather calloused to the plight of others, but will try to hide this somewhat at first. The later in the game she's encountered, the more she opens up, eventually asking the characters what motivates them and why they care so much about the world. She will find their answers to be bizarre and nonsensical. Initially unknown to the characters, she secretly harbors an intense disgust with the world and all those in it, and intends to do something about it.

At some point during the game, the characters will enter a town (New or previously visited) and find that it's entirely abandoned. Not a single NPC to be found. The town will be shrouded in an unnatural darkness and it will be eerily calm and quiet. There wont be any background music at all, perhaps just the ambient blowing of the wind (Which might sound like whispering is you listen closely). While wandering about the empty town, the player will come across the same girl from before. When the characters near her, she'll retreat into an old dilapidated house that would be locked at any other time.

When the characters enter the house, they'll find it to be old, decrepit, and most noticeably devoid of the girl. Exploration of the house will initially yield nothing but old, broken furniture, cobwebs, other types of debris, and maybe a few helpful items. Somewhere in the house is a secret passage the player must find before continuing.

The secret passage, when found will lead into a typical dark cave. Not much to explore here, just a path that leads straight ahead. Waiting at the end of this path, is the girl. When questioned about the strange events occurring in the town, the girl will explain she used her newfound power to make everyone simply "go away" and will show her displeasure of the fact she can't do the same with the characters for some reason. She will continue to explain that the source of her power is a mysterious stone or other object she found while exploring the house (Perhaps here she'll delve into a tragic past where the house turns out to be her only location of solace, or she could just simply be a twisted girl with a fondness for exploring abandoned structures. It currently doesn't matter). She'll then announce she's going to destroy the characters and thoroughly enjoy herself as she does so. A boss fight will ensue. The girl will primarily utilize offensive PSI abilities, perhaps putting up a defensive PSI power every so often. It shouldn't be a difficult fight.

When defeated, the girl will become enraged and will begin to draw more power from the stone in order to destroy the characters. She will end up drawing too much power and the stone will shatter. It is at this point there will be a distinct change in atmosphere. The light will diminish and the background music will be replaced by unsettling otherworldly sounds, perhaps a deep growling/breathing. After this, the girl will begin speaking in a manner similar to the following. Each line represents a single progression of the dialog. This is simply an example of what she might say.

"Aah..."
"..oooh.."
"W-what is this?"
"M-my head...it...hurts."
"What's happening?"
"Aaagh..."
"...nnngh..."
"I can't...think.."
"No!"
"Graaagh!"
"So much noise!"
"Make it stop!"
"Aaaaagh!"

The girl will flee to the next map, gibbering and crying. With nowhere else to go, the player will move onto the next map after her.

The next map will consist of a long narrow rock catwalk and the background will consist of blackness, with perhaps a red light emanating from the very bottom. The creepy ambient sound will continue. As the characters carry on down the path, they will encounter ghostly forms of the girl that can be talked to. They will each say something different, mostly just incoherent madness and disjointed rambling. A few examples are as follows.

"It keeps talking, saying the same things...over and over...but I can't hear what it's saying..."

"My body is numb...the only thing I can feel...is pain."

"Make it go away...make it go away...make it go away..."

Eventually to player will make it to the end of the path, where the girl will be found, crying. When talked to, she will begin to growl and snarl like a wild animal and attack the characters in an apparent rage. Another boss fight ensues, playing out almost identically to the first encounter with her, except tougher and the background will consist of an undulating darkness. The battle music will sound like heated whispering or something appropriately creepy and subtle shapes may be seen in the background, such as the silhouette of a tall twisted humanoid figure looming over the girl. The incoherent gibbering may also carry on during the battle. When defeated this time, the battle output text will state that her form vaporizes. The boss fight moves into its second stage. 

The new boss graphic becomes a wispy extreme close-up of the girl's face, her expression contorted into a look of terror and agony. The background becomes more disturbing, perhaps containing twisted faces and other unsettling shapes that phase in and out if possible. The battle music will consist of screaming and roaring and other otherworldly sounds put into whatever form. The boss' attacks will ignore any defensive PSI abilities and will either do damage or cause abnormal status effects. None of the attacks will contain any battle text, except for maybe "Something strange is happening." As the boss takes damage, the girl's face twists and distorts more and more. Finally, after a difficult battle, the face and the background will begin to swirl and warp and act very erratically. The characters will hear a voice, but not the girl's voice. A new one. It will say:

"I am...
...always..."

The boss graphic and background will seem to melt away and the battle will conclude. After the fight, the player may then explore a room beyond where the girl had been and find a powerful piece of equipment or key item, depending on the boss' significance to the plot. Upon exiting the cave and the house, the town will have been returned to normal. The inhabitants will be back form whatever it is they had gone, and will probably have a thing or two to say about the experience.

What is this boss? It could be anything. I will purposely leave it open for extrapolation. It could be the return of Giygas, it could just be an echo of his power, or it could be something else entirely (I like this one personally). There is one thing I will say for certain though, it is a terrifying ruinous power that has ascended beyond the use of simple PSI power. Its abilities lie beyond mortal comprehension.