This one requires a little bit of backstory as to what Ori is- they're a spirit (Therefore not bound by the same regulations as regular living beings on what they require to live.), and at various points they swim underwater, yet cannot breathe and will eventually drown without the use of the Water Breath upgrade. This begs the question- why does what is essentially a ghost need oxygen to survive underwater in the first place?
Fridge Brilliance that while Ori is a spirit, they're specifically the spirit born from an above water tree, and they were presented as a leaf at first. As such, it makes sense that they would have some of the same traits. Plants that don't grow naturally in water will drown if they are given too much.
The game calls Ori and their kind "Guardian Spirits," but they aren't really spirits in the modern English sense of being incorporeal beings without physical bodies - they're closer to The Fair Folk or Youkai, supernatural creatures which are bound to a location or concept (In Ori's case, light), but can still have physical bodies. Ori clearly has a physical body - they're affected by other things that shouldn't affect an incorporeal being either, such as gravity, walls, and just plain physical damage. The beginning of the game also shows Ori eating real food, and Naru giving the last fruit to them just before her death heavily implies Ori needs it to survive. Whether they can live indefinitely on light energy alone, or whether they need it instead of / in addition to food and water is unclear.
Each tree spirit had their own ability that Ori ends up learning, save for one; gliding with Kuro's feather. Why is it that this skill is gained in such a different way? Because it's one Ori had since the beginning of the game, we first see them as a leaf/feather, gliding on the wind, and later, during the bridge-building cutscene in the prologue, they are briefly seen actually gilding with a large leaf. Ori just needed something to glide with after manifesting their current form, and they couldn't find a suitable leaf because the forest is dying.
If one watches the prologue carefully, during Ori and Naru's Good-Times Montage, one notices it gradually turns from day until night. In a way, it's marking that the good days are coming to a close before the fateful night Kuro attacks the Spirit Tree.
Naru being a playable character in the final act becomes a fitting Book Ends when one realize she was playable in the beginning. In a sense, this is her story, and the way she "defeats" Kuro is by appealing to her motherly side.
The implications of all the Spirit Light containers lying around across Nibel. At the early stage of the game, small ones can fill a large portion of Ori's XP bar while large ones can practically fill it entirely. When one considers that Ori at level one with just one of the abilities that come later is likely representative of the 'average' guardian spirit, and that Kuro's attack on the Spirit Tree had sent most of their kind scattering into a wilderness that was soon becoming very perilous to traverse, this basically means that each container is essentially a gravestone, showing the resting place of a hapless spirit who succumbed in some tucked-away corner, fell onto a bed of spikes, drowned in a deep lake or a pool of corrupted water...
Unlikely, since we already see the graves of the other spirits, the small spirit trees Ori gets their extra powers from.
While Kuro is clearly the most persistent of them, all the creatures you run into seem to have it out for Ori by default. The major twist of the game is that Kuro actually has fair reason to be attacking you, since you were created by the one who (accidentally) killed her children. From what we see of the Spirit Tree's search, it was quite thorough: who's to say some of the other 'monsters' don't have similar motivations?
The forest was always going to be devastated once Ori was lost. It took years for the Spirit Tree to find out the damage done by him setting the night sky ablaze. If Kuro hadn't forcibly halted him, there is no indication that he would not have continued to set the night sky ablaze until Ori came home. Which wouldn't work since it was being raised by Naru to whom the action was a threat. There is a reason for why the narration says Kuro was protecting her last remaining child, the Spirit Tree was an active threat.
At the beginning of the game, Kuro attacks the Spirit Tree and every last Spirit Guardian she comes across, including Ori. The Spirit Tree keeps calling Ori his child, and the other Spirit Guardians could be considered his children as well. Because she attacked due to the tree accidentally killing her children, this extremely caring mother turned into the very monster she thought was fighting against as she wound up killing many of his children as well as Naru and the Gumon indirectly. She orphaned Ori by making their adoptive mother starve to death and almost completely killed off a race that had nothing to do with the incident.
