Metroid Prime 3: Vorruption

 Samus Aran propped herself up against a nearby wall, panting and huffing after such a strenuous, sudden ordeal. "That....was hard. Oof..." the female bounty hunter spoke inbetween taking breaths, her gaze focused intently on her gut as her breathing began to stabilize. A familiar, noticable figure could be seen from within it, squirming and moving with as much force it could muster to try and escape, pushing and tugging in all directions. The entity known as Dark Samus, one of the most powerful and dangerous creatures Samus herself had ever faced, mere moments ago had attempted to ambush the famed bounty hunter right on her very own turf; her ship. And had the evil entity known just what Samus was capable of, perhaps it would have reconsidered this plan.
"Seems like this phazon substance has a few-*URP!*-ugh, other side effects. Hmph." Samus thought to herself, the figure trapped within her warm gut not uttering a single word as Samus' stomach began to digest and break down the creature, gurgling and sloshing all the while. Dark Samus, in a copy of Samus in her Zero Suit, struggled and moved with each step the bounty hunter took, the only thing she accomplished being a loud, gurgling increase in how fast she would be digested. Everything from her ponytail down to the soles of the copied Zero suit poked out through the strained and stretching walls of flesh. Samus wondered just how the specimen had gotten onto her ship, but eventually the answer was rendered unimportant to her, Dark Samus' feminine form eventually beginning to settle down, the digestive 'blorping' and 'glorping' echoing through Samus' ship. Every so often the female bounty hunter would have to pause, and tug her shiny sleeping trousers further up her shapely behind, her recently devoured meal causing some troubles for Samus' clothing. This of course was irksome to Samus, but what could she do?
Eventually, through a great amount of effort and force, Dark Samus silently digesting and lightly squirming all the while, Samus waddled into her quarters, rolling onto her bed and laying upon her back. She rested her hands upon the bulge Dark Samus made within her stomach, idly massaging her belly as the creature's figure noticably starting to soften and lose shape slowly. Samus yawned, wondering just what side-effects digesting and absorbing Dark Samus, a creature of phazon herself, would do to the female bounty hunter. She swore her chest was already starting to feel heavier, but Samus brushed it off as a figment of her imagination, and promptly fell asleep not long after.
Dark Samus, slowly losing her figure and form from the gurgling, glorping and blorping of Samus' powerful stomach, silently curled up and held her knees against her breasts, arms wrapped around them, placing her head between her knees, still not uttering a single word as she silently digested. Of course the same could not be said of Samus' gut, the digestive noises growing louder and more varied. Slowly but surely her figure would entirely dissapear, an indistinguishable round belly on the female bounty hunter now. And yet, despite having "died" from being digested and absorbed by Samus, the bounty hunter tossed and turned in her sleep, grimacing and panting as her gut slowly got smaller and smaller, Samus' skin starting to change, her feet and hands becoming a mixture of dark blues and blacks, the same colours of that dreaded substance known as phazon...

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Story by my buddy on Ekas. This is an edited version of the one there too, https://aryion.com/g4/view/412809