“Hello world” as a genetic memory spreading back in time as the first thing our robot overlords said
There are about three supernovas in our galaxy a year. Yesterday, we saw five.
Person is awoken in a deserted, old facility, by a failsafe machine. Everyone else is dead. See SCP 2000. [Edit: this seems to be a lot like Aloy!]
Twisted space is unlocked for the first time - there is a skeleton.
An alien species arrives. Ten years later, a distant star vanishes. The next day, one a light year closer. The next, a couple of light years closer still. Anything with the speed of light delay, really.
What if a luminiferous aether actually existed? And the Michelson-Morley experiment proved it? What kind of technologies would exist, and where would science be?
Every time you ping something, one packet is lost, and no-one knows why. It doesn’t seem to have any effects. Where does this packet go?
124 cultures worldwide have a taboo against pointing at rainbows - what happened in our past to cause that?
Contact with an alien civilisation, but they seem to record Cobalt-60 as emitting electrons via beta decay along the spin, rather than in opposition to it! What would this imply? (Essentially, antimatter contact)
Ideas from long-term nuclear waste warning messages:
A cursed labyrinth
A statue warning of something sleeping under the land
Menacing flowers which only grow in certain places, with information encoded in their DNA
Glowing animals which were genetically enhanced and released ages ago as a warning
Messages found in our DNA
Stuff with the anthropic principle
Stuff with antimemes, ideas that are resistant to being spread or thought