After The End, Flowey is brought to the surface too in a little flowerpot. Frisk totes him around everywhere. It's like Lilo and Stitch with more ambassadorial responsibilities.
Frisk went to bed in the police station, after the Emergence Event, in a police department T-shirt and empty-handed. When they came for them in the morning, they had a flowerpot and a talking buttercup.
There was a reason Frisk's foster families had complained about escapes, but lacked proof.
One of the monsters was sitting with Frisk, and casually blocking the flower's every attempt at casting bullets at the people trying to sort out everything.
Frisk only said two words, at a whisper, and to the flower, that day. They said, "Remember kindness."
It took a handful of days for Flowey the flower to apparently give up on shooting everyone with seed bullets, but the monster bodyguard remained. Proof that the monsters were perfectly willing to be peaceful. Every minute of the day, if necessary.
Flowey was, in brief, a menace. It filled the negotiations with a constant diatribe about the ways it could use a human soul, about the ways it could kill everyone. Frisk simply petted it and laid gentle kisses on its petals until the diatribe fell to a low mutter.
Frisk had mercy for everyone. Even the worst of the monsters.
Counsellor Lyme found Frisk and Flowey in the gardens of their new mansion. Frisk was their usual silent self, shaking their head at the flower.
"I could. I could leap free and kill a human!"
Shake shake.
"Here comes one, now. Don't you look delicious?"
Shake shake. Frisk patted the flower. Petal by petal, until the plant sagged.
"Urgh. Fine. I'll stay where I was put. As agreed." Flowey resumed its usual muttering, but the effort seemed to be lacking. It kept revisiting the phrase, see if I won't or everyone deserves it.
Frisk waved 'hello' and brought out their special tablet from their backpack. With a few swift taps, they were able to say, "Therapy is working. Flowey is getting better," through the tablet's speakers.
"...kill you all and take all the souls, see if I won't," muttered Flowey.
Frisk laughed and tapped out, "I know. It's disturbing. Doctor Alphys has been helping, too."
Oh yes. The monsters had perfected ways to isolate qualities of the soul. "Really? More determination?"
"No," 'said' Frisk, tapping at their tablet. "Something else. Kindness. Love. Compassion. We try new mixtures every day. We're eroding Flowey's bitterness and hate."
"...you'd deserve it all. Everyone deserves it."
"Slowly," amended Frisk. They leaned over to kiss Flowey's petals.
"STOP BEING NICE TO ME!"
Shake shake.
It was obviously going to be a very slow improvement.