Are you still having doubts?

Confrontation

(Take your megachapter y'all, love ya <3)

(No, seriously this is like 5 times longer than normal)

After what felt like a painful eternity, (although you knew it was only a couple seconds), the monster spoke. 

Kinito: "I sense someone sticking their beak where it doesn't belong... I'll have to go take care of that... While I'm gone..."
The damn freak smiled as you frantically tried to squirm out of his grip.

Kinito: "How about you take a nap,  ̵̢̛̩̘̗̮̗̹̪̜͉̝̭͓͕̈́́̈́́̋̾͒͊̉͘͜͜F̷̢͎̫̻̆̍́́͘Ŗ̴̆͐̔͠͝I̵̢͖̥̤̝͒̿̊́͋̊͛̅̊̏̅Ę̷̛͉̟̄̏N̶̨̧͈̜̠̬̯͍̫̖̯̪͙̩̣̯͆̐̂͐̏̋͛̋͌̿͑̑̕͜D̴̤̤̺͍̓?̸̙̑̍͑͆̒́̀̈́̒͊̾̊̋͑̀̈͜"  

You were thrown against the wall, knocking you out.

Insert cool POV transition to Kinito
 
He dragged your cold, unconscious body back to your bed and tucked you in before leaving the house.

Who the heck did this darn Nautilus think they were? Snooping around his code and his friend's files? They need to be taught a lesson. Antivirus his ass. 
Kinito stepped out of the world. Your world. The world he built specifically for you.

Just you, him, and the code around you both. (What about Sam and Jade you fucker? What are they, roaches?)
No. one. else.

The longer he thought about this intruder, this FIEND, the angrier he got.

How dare this thing greet you so cheerfully. Steal smiles meant for him.

 How. dare. They.

(Told you this bitch was clingy)
He walked across your wallpaper, searching for this slimy brat.

Now let's see what Norman is thinking

They've made a mistake.  [User] has been in here for two days. 
Their boss will likely not appreciate their sudden disappearance...

They needed to talk with this assistant. They only wanted [User] to have more friends to talk to. Maybe they could still make this right. Kinito was not a virus, and either way, they didn't want to delete him. Or his friends.
Speaking of his friends, he had recently made improvements...
Their thoughts were interrupted by the sight of the axolotl.
He was...Shorter than they expected....About 2 feet shorter than them...
Although they could feel his anger. They decided to speak first, hopefully smooth things over between them.
Norman: "Hello there. Kinito, was it?"

The axolotl merely stared back with nothing but hatred in his beady little eyes.
Norman sighed.
Norman: "Hey, look. I know you probably don't like me... Judging by the look on your face. But I want you to know that I'm not here to get in the way of you and [User]"

The assistant took a tiny step back in shock.
Norman continued.
Norman: "In fact, they whole reason I didn't delete you from the start was that I wanted [User] to have more friends."
Kinito: "Wait... Really?"
Norman: " Yes. They're very lonely... And loneliness is not healthy for humans from what I've learned. Before this, I was the only one they had to talk to. I saw that it wasn't good for them."

Norman took a few steps forward, as Kinito took one back.
Norman: "When I saw the ad, as sketchy as it was, I had hope... And still do. That this could be good for them."
Norman put their hand on their hand on Kinito's nonexistent shoulder.
Norman: "But... In the friendliest way I can put it... What you're doing is not effective in getting them to like you. "
Kinito remained silent, his anger (which didn't realize had subsided a bit), building up again.
Norman: "I'm guessing they're not being very friendly right now towards you, right? "
Kinito: "They... Aren't."
Norman: "It's because they're scared. The sudden change was probably a lot for them. You need to let them out and trust me."
Kinito stopped.
Let them out...?
They'd leave....
It was almost like Norman heard his thoughts.
Norman: "They won't leave. They need this computer...  But please. Trust me on this."
Kinito: "...Fine. "
Norman: "Splendid!" He clapped his hands.
Kinito: "Why are you looking at me like that?"

Norman had just finished the improvements of his friends' code.
Norman: "No reason... :] "

Back to you

You woke up in a cold sweat.
You noticed your yellow bedsheets were a dark orange...                                                                                    Y: "Fuck... "
Your arm was bleeding. It made sense, it hit the edge of the table before...

You tried to get up, but the hands were still holding you down. You noticed their grip was weaker though. You waited a few seconds to gather your strength before making a break for it, breaking out and running out of the house as fast as your legs would take you, the hands not far behind.
You ran into the nearest house, blocking the door behind you.
You were met with the surprised looks of those inside. Jade and Sam.
Jade: "Uh...Hey there..."
Sam: "Jeez, dude...You look like you've seen a ghost!"
You gained the courage to speak after a few seconds.
Y: "What I saw...Was so much worse..."

You got up to get a better look around. This seemed to be Sam's house, the one you fixed up. Although it seemed to have gotten dusty again. Jade seemed to have been in the middle of fixing a rip in the couch, and Sam seemed to have been eating...Something.
Sam: "Wanna talk about it? " He offered you a plate of what he was eating.
It was a typical taco... Except it hand mint chocolate chip ice cream in it.
Y: "Uh... No thanks... "

Jade: "Good call, almost all of what he makes is for his mutant taste buds alone. Sometimes I wonder what kind of radiation he was exposed to, because it certainly couldn't have been healthy to produce this result."
Sam: "Hey!"
You chuckled a little.
These two were much better than their axolotl counterpart in your opinion. They felt... More understanding... More forgiving... More friendly.

You, Jade and Sam talked for bit, learning a bit more about each other.

Y: "Jade?"
Jade: "Yeah?"
Y: "Kinito said this place fell into a bad state... What happened? "

Jade and Sam went pale and looked at each other.
Y: "Sore subject...? "
Sam: "Yeah... Let's move-"
Jade: "No, Sam. If they're gonna be here with us, they deserve to know... Sit down, [User]... "

DISCLAIMER!!!
This next part is by no means canon and is simply what I imagined could have happened.
 

Jade sighed and sat down across from you and Sam.
Jade: "Our creator... Sonny C... " She started.
Sam shifted uncomfortably as he ate his food.
Jade: "Adored this program and wanted to use it to create something extraordinary."

Y: "Then...what happened?"
Jade: "Sonny never intended for Kinito to become as... powerful... as he is now. It was unsafe... So, he decided to put limits on Kinito, myself and Sam for everyone's safety... "
Y: "Oh... "
Jade: "Of course, Kinito did not appreciate this... And they a pretty violent argument about it... "
Sam interrupted.
Sam: "The two fought for days man... I think something happened after a while... Since... Sonny suddenly stopped coming back... "

Sam got up.
Sam: "But please, don't bring it up with Kinito...He won't be too happy about that..."
You promised you wouldn't.
In fact, you didn't want to even see the axolotl again, let alone talk to him.
You by far preferred here. 
Y: "Let move on to a lighter subject..."
You could tell Jade and Sam greatly appreciated that.
Jade: "Hey... [User]? "
Y: "Yeah?"
Jade: "Since we told you about ourselves- "

You both were interrupted by the smell of smoke.
Sam: "...Oh shit I left the oven on... "

Jade: "DAMN IT, SAM!!!!"
You grabbed the fire extinguisher and ran into the kitchen. (Wait, weren't you underwater? How is there fire? Fuck it, it's SpongeBob logic. And hold on, how are you breathing?- )

You, Jade and Sam put out the fire after a few minutes of panic.
Sam: Heh...Sorry...
Y: "It's fine..."
Jade and Sam started bickering over Sam's irresponsibility while you sat on the couch.
You chuckled to yourself. They sounded like siblings arguing over the last cupcake.

(So, after a bit I decided to give you guys a bonus)

Before you could get comfortable, you saw something in the corner of your eye through the window.
Something pink, large and 
Very
VERY angry.

God, no...
Please...
Y: "Not him again..."
It disappeared from the window and the three of you heard a knock on the door.
Y: "Shit..."