Cleaning time... the Chozo thought
Samus didn't realize just how much a DNA augmentation would hurt. Having what controls each one of your cell's functions, having it cut to size on a microscopic level...well, it hurts like hell.
Despite the pain, Samus remained conscious during the ritual. At least, what seemed to be like consciousness to her...
Samus regained her Varia Suit; that familiar case of hardened alloy, circuitry, and hydraulics. And yet...something still didn't seem right, like an itch that can't be scratched. Samus ignored it, still raw from having her DNA ripped to shreds and fused back together.
Gently, she moved around in her suit, somewhat unaccustomed to the elegance of the controls that the fusion suit simply did not have.
"Is it done?" she asked the Chozo.
"Yes" he said, with an almost wicked smile.
Samus, still a bit dazed, didn't detect the slight malevolence in his expression, and with a simple "Thank you", she summoned her ship and entered her cabin.
The Chozo chuckled to himself as the gunship flew away. Into a concealed microphone, he said "It's time..."