TLDR: Warp core negative time interval, Hatchling's brain is uploaded with all previous loops as they wake up.

When traveling through black hole to a white hole, a negative amount of time passes. Nomai warp cores utilize black and white holes. The more power is provided to a warp core, the bigger the negative time interval becomes (this is demonstrated in the High Energy Lab).

The ATP makes use of the supernova to provide its advanced warp core enough power for a -22 minute interval between entering the black hole and exiting the white hole. Both holes are opened in the core of Ash Twin. They are not intended to be used to transport matter, though. The information stored in the masks is sent through them, and the same masks retrieve that information 22 minutes earlier and then send it to whoever/whatever is paired to them. The masks also receive a steady stream of updates from their partner.

At the start of each loop, when the Orbital Probe Cannon receives information from the previous loop, it takes this as a firing command, knowing that in 22 minutes, the information it receives will be sent back in time (this means that during the first loop, the probe didn't fire, but during the second, it received a blank data upload that spurred it on, or perhaps the Sun Station is somehow linked and sent the first request). The probe cannon randomizes its firing angle every loop, presumably using past loops' data to ensure it doesn't repeat an angle.

The bigger, more blocky text is written by children with poor "handwriting."
Orange text appears in projection stone writings because there are two linked stones, one in each location, which send text to each other. The orange is text that has been received from the other side, whereas blue was written on the side you're reading from. If you travel between points where the stones are linked, you'll see the colors are flipped. You can also see that all the modern received text on the Vessel is orange.

The solar sail.
The Stranger can detect when the supernova is imminent, much like the Sun Station. When it sees it coming it opens a solar sail that will propel it beyond the reach of the blast. It has to divert some power to opening the sail, which causes a brief flicker. The movement is also what destabilizes the dam (you can see this with your scout, it has a structural integrity reading like on Brittle Hollow, but it doesn't start ticking down until after the sail is opened).

Being outside the supernova's range means Hatchling doesn't die to it, but they also don't receive any memories from beyond the ATP activating 22 minutes after they wake up, so the player perceives this as the loop restarting. In reality, Hatchling could have lived a while longer there, but the next loop version of them wouldn't remember any of it.

The structural integrity of the crust is being weakened by Hollow's Lantern, which started having increased activity around the same time the Sun did (this is relayed by a Nomai computer on Hollow's Lanturn).

Hatchling, Gabro, Orbital Probe Cannon
The Nomai computer in the ATP refers to their statues as "Timber Hearth Statue", "Giant's Deep Statue", and "Orbital Probe Cannon Statue"

The Owlk were the first intelligent species in the Outer Wilds. The only signal the Nomai received was the brief window opened by the Prisoner, and by the time it reached them, the Owlk had stopped spending time in the material world.

The Nomai were never aware of the Stranger and the signal had been cut off again before they even reached the Outer Wilds. Essentially, they warped out of the range that the signal was active in.

The Hearthians' genetic predecessors were alive during the Nomai's time, but were entirely aquatic, and ghost matter is neutralized by water (you can see this in the cave on Gabro's island just after it falls from space), so they survived the Interloper and evolved.

They're not. The eye is creating reflections of them based on Hatchling's consciousness. The new universe is being born in the image of them and everything they care about, and cases of extra special bonds manifest themselves physically.

It's not outright stated, so there are a few ways to look at it.

Clunky option:
Any individual on the quantum moon can be treated as quantum themselves, meaning they are technically in all locations at once. When one collapses the possibilities into one location, they're only collapsing their own perception, and still exist in a quantum state for everyone else.
Solanum died in the ghost matter incident at all 5 planets, but lived at the eye. However, time only passes for her when the moon's at the eye and even then, time seems to work different there.

Marginally Cleaner option:
The ghost matter incident happened as Solanum was on her way to leave the Quantum Moon. As she was dying, she stopped perceiving her surroundings and entered a quantum state, where 5 versions of her died and one lived. This is why she suspects she's dead, and why she doesn't try to leave the 6th location.
This theory still requires that the conscious version of her at the Eye doesn't hold the moon in place, and that either Nomai have very long lifespans or time passes differently at the Eye.

Dialogue from Hal reveals the ship log is built from pieces of the Nomai statue you are paired with. You and the ship share the mask linked to the Timber Hearth Statue, but since your brain and the ship process information in different ways, you don't have text in your memories and the log doesn't have your memories in its text.
Loops where the ATP is shut down are explained by gameplay convenience. Technically, Hatchling shouldn't remember anything from that loop when you load from last save, but you as the player already saw it, and the game can't erase your memory, so it goes on the log..

The Bramble is almost comparable to a disease. It sends out seeds and they grow into their surroundings. The planet Dark Bramble was once a different planet (from the looks of it, something icy), but the Bramble grew outward from its center, eventually destroying it.

The seed on Timber Hearth clearly leads to Dark Bramble, but the Bramble presumably didn't originate from the center of the ice planet, a seed must've gotten lodged inside. Whenever you back out of a seed, you fully exit Dark Bramble (so if the hole were big enough, you could enter the Timber Hearth seed, but then go back through and be at the main one). Presumably, once an external seed grows enough, it becomes its own central hub, and no longer links to its seed of origin.


To be honest this one's not fully explained by the game but it's not as central to the plot as the others, so I'm reluctant to call it a plot hole.