WMG for the anime short film Shelter:
It was Mars that crashed into the Earth. Mars' diameter is just over half of Earth's, meaning it is small enough to be the body we see in the reflection on Rin's shuttle when she is first launched. The map inside her shuttle at the end shows it has passed Pluto and thus left the solar system, which also suggests whatever destroyed Earth came from within it
Alternatively, it was Melancholia that destroyed the Earth.
Spoilers for both works, obviously. In Melancholia, it is shown that the planet Melancholia needed months before it had approached the Earth (a diagram in a scene showed that Melancholia was first detected in the Earth's orbit in March, and the fly-by were predicted to happen in July). Since the film never showed anything outside the mansion/estate, the outside world might be in a state of chaos. The film also did not give hints to the year it is set, so it might be argued that the film could be set in the future. Also, it is mentioned at the film's main page that even a fly-by could be potentially dangerous, as disasters could happen. In Shelter, a newsreel had shown Tokyo in chaos. That might have happened during the fly-by, just before Rin's departure. Also, the events in Rin's flashbacks might be anachronic as they are fragments. Here is my theory of how things went down for this WMG: Firstly, Shigeru might have suspected that the calculation of Melancholia's fly-by might be wrong, so he decided to create a spacecraft specifically for Rin, months before the fly-by, just in case that the predictions of the collision might be true. And then just hours before the inevitable, he had prepared Rin for the launch, and then moments before Tokyo's collision, Rin was quickly sent into space. This WMG might not make sense since the object was shown to be red and smaller than the Earth, as opposed to Melancholia, which was blue and larger than the Earth, but oh what is a WMG...
Shigeru died three years after sending Rin to space. As shown by Shigeru's blueprint in the flashback montage, Rin was seven years old when he started constructing her shuttle and she doesn't seem much older when launched. However in the present day the 17-year old Rin hasn't received any messages for 2578 days, which is just over 7 years. Either she was receiving automated messages to help her acclimate over the first three years or Shigeru was somehow able to keep tabs on her before dying
Rin will ultimately be saved. If Shigeru could construct a spacecraft capable of sustaining life for at least seven years with a built-in virtual reality, then the plot probably takes place a considerable ways into the future. It stands to reason then, if technology has progressed to such a point, then it may be possible that either some portion of humanity has been able to evacuate earth and/or has been able to establish space colonies. Survivors of earth's destruction or extraterrestrial colonists might have detected Rin's craft and were the ones who sent her the message at the end of the story, telling her that they were en route to pick her up.
- The short takes place between 2073 and 2076 if Rin's tablet's serial number (2066) is any indication, assuming that was the year she was launched. While the main part of this WMG is still possible - and likely, if you consider Shelter to be a prequel to Worlds - the last part is Jossed: the letter came from her father.
Shigeru started work on the shuttle when Rin was 5 and she was launched when she was 7. The birthday cake in the flashback only has six candles, meaning it was her sixth birthday. Yet the blueprints state her age as 7, which is presumably when Shigeru planned to finish building the spacecraft. Rin would have had 3 years worth of (automated) messages to help her acclimate to her new world, followed by the seven year drought we see in the short.