The Sundered Goddess and Queen of All Magic, Twilight Sparkle, has reunited with one of the 24 Fragments of the Sundered Goddess: Okami Amaterasu. She has to fulfill all of Amaterasu's duties. Finding a foalsitter for Amaterasu's son, Chibi, is one of those duties.

If only Chibi weren't so cute.

This is an AU where many cultures have physical gods as rulers or patron deities. More information and world-building can be found in this thread. The story should be readable without reading the thread. The thread just offers a ton more background info.

This is a quasi-crossover. It features Ammy and Chibi, but they are given different back stories and treated as parts of the universe. They never had their adventures in Nippon, hence the lack of a [Crossover] tag. Edit: moderators made me add the crossover tag.

Characters not tagged: Dinky Hooves, Cadence, Shining Armor.

Changed rating to teen.

A Metroid Crossover

A meteor, resistant to magical manipulation, crashes in Equestria, Planet Equis, and soon spreads an unknown poison throughout the land. Containment is all but failing and the Princesses have little power to stop the spread of the Great Poison. The Elements of Harmony are of little use as no knowledge exists of this threat that consumes all life. Help comes from a certain Hunter, clad in metal.

Samus Aran will not only fight for her life as always, but her own sanity as well as these ponies that she begrudgingly starts seeing as allies. New horrors and abilities await her as a reason to fight slowly festers within her, possibly unlocking something she had been denied for so long: Friendship.

Notes and Resources:

This takes place after Echoes. The events of Corruption will have not happened yet. In terms of MLP, consider everything up to and including the Crystal Empire. Princess Twilight does not exist here, etc. The official Metroid Timeline can be found here.

As well, this story references the manga in many places. Reading of it is not required and I try my best to explain the context, but if you're interested, both volumes can be found here.

EDIT: This story was written over two and a half years, beginning in 2013. You'll probably notice the difference in writing as the chapters progress.