If...
No signs of distress as far as the world actually ending. In fact, we see planes grounded, most lights out, and ever increasing evidence that most humans knew their end was coming quick, accepted it, and in a very in-human manner, left the world neatly packed so that it didn't fall apart right away.
This must be a planned act. There should be records of the plans, somewhere.
No record of humans disappearance is left. Our space being learns that it all took place in a day, but what happened during this day is a mystery. Almost as if no one was allowed to record what was about to happen
The plans must exist somewhere, and even communicated to the population (at least the parts they needed to know※). Otherwise, there should be signs of chaos. Now, you will not find news about it, because who are those news directed to anyway? - If we were leaving earth, we would systematically reduce many systems to a minimum, including news reporting.
※: You may also not find records, because they may have not told people that they were going good-bye. Instead, they may have said some other plausible excuse to keep them in line until the time comes. People may have knew their end was coming, but from some natural disaster, some impending war, a pandemic, etc... Not from a disappearance trick.
On that note. I will pretend that this visitor has been analyzing years of radio broadcast to study the languages of earth to a point where it can understand spoken material. The visitor could have some idea about written language if they decoded video signal...
However, as far as we know we have not broadcasted via radio or television the internet protocols with enough detail to implement them (Or it was a very boring program that nobody watched). Based on that, I would say he does not have compatible technology (baring any Independence Day plot hole). He may or may not have an idea of how to use an earth computer... but even if he manages to do so. The description suggest that the servers will be down.
For abstract: the records maybe there, the visitor just cannot reach them / understand them.
Plants are still there, as well as bacteria, and some animals but as individuals.
Does not sound right. Are you saying that animals no longer form groups?
Human conflicts were taking place, as we have not made much more progress than today. However, all events from now, till 2031 when our friend arrives, would be realistic and feasible to our current events know.
In that case, it is expected that world peace has not be reached. This complicates how to make a plan to more all humans.
what would be a good direction or themes I should explore with how humans actually disappeared?
Not everybody did agree. Some wanted to stay.
You say humans knew their demise was coming. However, that does not mean they all agreed on what to do about it. If such plan required unanimity of all the population, it probably would not have worked. Therefore, we can assume some people did not want it to happen.
Done from the shadows.
Such coordinated disappearance trick requires a world government or something similar※. We are not talking of a situation where everybody who did agree left earth... we are talking of a situation where everybody left earth, willingly or not. “They” did this to them.
※: The United Nations, a similar near worldwide nation’s coalition, a very powerful country able to pull this off by force, or a shadow government that has been controlling the big decisions from some time now. Perhaps an alien nation or supernatural beings qualify too.
Depression
The world is going to end. People know it. This means that in the Kübler-Ross model, most people are past Denial, Anger and Bargaining. Thus, I would expect many people in Depression. People do not want to bother to do anything, there is no point, and the world is going to end anyway.
Suicides would have been common. A reflection on that: what happened with the corpses? Did they disappear too? What about cemeteries? It is hard to imagine that humans would have gone into the trouble of getting rid of these.
Depression
Production of not essential goods and services has stopped. Either because resources are being diverted to do the disappearance trick or because... why bother, right? - This means that economic activity was going down for a while, so unemployment was on the rise. Because of that, it was hard to get credit.
If this was all part of the plan. We should assume that there was a preparation period prior to the programmed depression. This period would have entailed the creation of plans to ensure the safety and wellbeing of the population. Therefore, I would expect curfew, mandatory savings, and strong surveillance. [I do not find that far-fetched at all]
Where did humans go?
Underground: I do not think humans went to space. The visitor would have noticed. It is easier to think humans went underground. However, the time is short to make hidden bunker cities for the world population.
Not to mention the problem of stocking supplies to stay there for who knows how long. Perhaps cryogenics works better?
Animals are ok.
Mass murder: Consider a bio agent (I am thinking bacteria) designed to target and consume human DNA at rapid pace. Released on the water supply (because why not?) it could make humans go puff relatively fast※. However, not done in one day fast, unless, of course, you sprinkle some science fiction on top.
If something can prevent animals to form groups, it must be a bio agent, right?
※: About a week or two is viable. Disregarding dry remains, those take decades. Therefore, the visitor would have found a bunch of skeletons and a very bad smell.
Wormholed away: Maybe they transported via wormhole the world population. In this scenario, humans would develop the technology to create wormholes in the near future (or it already exist, but it is a secret military project), they have to land the wormhole in a habitable planet, and perform mass exodus.
We may have taken animals with us, at least cattle and pets. Otherwise, animals would trive.
We are still on Earth: Perhaps humans did not go anywhere. We could have detected and crashed the visitor ship, and put the visitor on virtual reality. It is an interesting way to see what intentions it has with the planet.
In addition, the animal’s thing is a glitch.
Aliens did it: Another race took all humans away to save them / slave them / whatever them.
And the aliens had an alien virus that killed the animals?
Transcendence: We have evolved into being that do not need a physical form. Either by external aid or by our own merit... A branch of physics of which we did not know, and that was latent in what call human soul, has allowed what we think of a miracle.
And the animals... too?
Why is the world ending?
Given the target date (2031) it is possible to have a fossil fuel scarcity crisis※. That does not have to mean dystopia; it means growing opportunity for alternatives.
※: This is under the assumption that we are already past Peak Oil, and we will continue to deplete reserves, driving the oil price up. Furthermore, the demand also tends to increase. At some point, it will not be affordable for individuals to use it as fuel for cars or similar applications. I do not really know on what source for predictions to go with for this… in my opinion 2031 seems early, but possible.
We also have the predictions of climate change that points to a harsh environment in the future, from which there is no fast recovery path. Leaving Earth could be a plan to allow Earth to heal itself.
Finally we pandemic frequency analysis. For instance, we have a period of roughly 24 year in average between influenza pandemics. Being the last one in 2009, we can expect the next one for 2033. Note: that is just average.
Many predictions of the singularity point to 2028. The main argument is applying Moore's law and comparing with human brain estimations of processing power. Of course, that says nothing about software, although usually software tends to find ways to push the limits of the hardware very quickly.
