"Be careful what you wish for" will stick with us for some time. We wished to travel again, but never in circumstances that were forced on us this pandemic summer of the cursed 2020.
In half a day we had to research and buy tickets from Japan to Poland and prepare all the formalities. Japan has been discriminating foreigners for months now (travel wise, in other aspects it’s been going on for centuries), forcing legal visa holders and even permanent residents (10 years in the country plus) to remain wherever they got stuck, without a possibility of return to the country where they live and work.
In extreme circumstances though, such as family emergency or medical procedure, international travel restrictions can be lifted. Therefore, if it happens to you, the first thing to do is to reach out to your embassy. If you're lucky not to be Polish, they should pick up on time and be helpful by guiding you through the procedure. In case of Japan, you should get a letter from your embassy vouching for you and letting the immigration officer know that the reason for your travel is legitimate and they request for you to be allowed back.

During the pandemic, many airlines don't operate usual routes and if you need to travel ASAP, there's a good chance you'll need to have some layovers. After you have your embassy clearance, call the embassies of the countries you have layovers in. There's no use for your ticket if you need to pass through a country that won't let you travel further without a test, they take a while.
Mid-June, there were only two airlines going directly from JP to Europe - Air France and KLM. And this was not a publicly known information either. The chaos is overwhelming - airfare search engines and websites of the airlines show routes that are non-existent or cancelled, switching the dates and hours of the reservation as you go through, only to find out at the end that the flight you picked does not exist. Not to mention that every time you try again, the fare changes, sometimes to show triple (sic!) the previous price. Your best bet is to call an overwhelmed support line and have the agent walk you through the truly available options.
You managed to find a flight, you have your embassy's warranty and you head to the airport? I don't suppose it would be a surprise to anyone anymore that a mask is a must. Take some spare ones as there's a good chance you'll spend the entire journey wearing it. Most airlines allow you to take it off only for the meal.

The Kansai airport in Osaka, serving as a gateway to one of the most visited regions of Japan and usually serving 30 million passengers a year, was completely deserted. Ours was the only international flight, seemingly with all of the passengers being foreigners and either in a family emergency situation or leaving the country for good. The airplane was carrying only 40 passengers.
When you cross the EU border, suddenly everyone and everything seems way more relaxed. There were actually people not wearing a face mask at Schiphol, while in Japan you'd have difficulty finding someone on the street without one. On our entire journey we didn't have our temperature checked even once, there were no tests, no heat cameras gates, nothing. Boarding a plane in Amsterdam resembled more a sales event than boarding a plane during a pandemic, with the staff reminding the passengers every minute to keep their distance and not to crowd by the entrance.
On the plane to Berlin, all the seats were taken. There was no social distancing whatsoever. The meal on the plane was served in advance - everyone found a lunch box on their seat and no additional service was carried out.
You will be asked what your destination is more than usually. But truly, it doesn't mean much if your travel pattern is not "normal". We flew from Osaka to Amsterdam, then Germany and from there by car to Poland. We filled out a card in Germany indicating our destination in Poland but the authorities clearly do not share this information as nobody checked on us even once.

You exchange tons of emails with the embassy, send necessary information, follow up. You pledge to self-quarantine after return and not use any public transport upon arrival (what's the point of the latter one might ask? You have to test negative to enter so you can't share a disease you don't have. Not to mention you need to stock up and reach your house anyway. As a point of reference, Narita airport is over 50 km away from Tokyo city center and a cab costs an unbelievable 250€). They inform you that the Japanese Ministry of Foreign Affairs is aware of the situation and they will communicate with the airline. Ultimately though, you end up not knowing if they will let you board the airplane. The embassy says the final decision belongs to the immigration officer and they don't provide any additional confirmation or support. LOT Polish airlines is as useful as usually - you first need to spend minimum 30 min (confirmed on multiple occasions) on their support line with cutting melody (damn, it can't be that hard to fix this) and when you're blessed with someone picking up, their only response is that it's the passengers responsibility to know. During a pandemic and when travel restrictions change almost every day. It wasn't even clear what would happen if we're not allowed entry after landing in Japan.
At the airport in Warsaw everything seemed to be going well. We went through the security check and passport control with no issues. 20 min before boarding, we were called to the gate and asked on what grounds we are travelling. The staff only then started to take pictures of our documents with their phones (where's GDPR?) and nervously calling their counterpart in Japan for confirmation. Many questions, no idea about our situation and no previously arranged paperwork promised by the Polish embassy. The boarding finished (25 people aboard a Dreamliner, that went fast), the gate closed and we were still waiting for a confirmation. Our luggage was held outside the aircraft until the very last second. If only travelling during a pandemic wasn't stressful enough…
Finally we boarded the plane, our luggage was thrown in at the last moment too, and we flew back home with 23 instead of usual 250 other passengers aboard.

We arrived in Narita the next morning. The disembarkation was quick but the ground staff held us right by the gate. We were handled some paperwork to fill out and led down the chair-filled halls to the testing station. Japanese tested with a PCR saliva test. You need to spit enough saliva to meet a mark on a plastic tube (the Japanese provided a helpful visual aid of a Japanese pickle and lemon ;)), deposit it at the designated table and move on to the next checking station. As usual with the Japanese, there's probably 4 different points where the same information on your sheet is checked (go low unemployment!). You are asked whether you have Line, the Asian WhatsApp, which they use to contact people on quarantine, but nothing happens if you don't. Finally, you are being seated in a hall with hundreds of seats, awaiting your results with complimentary water and green tea. We waited for almost three hours for our negative results, but judging from the forums it can be anywhere between an hour and four. Overall, counting from landing, we arrived home 8 hours later.
Since you cannot use public transport, including taxis (but who would like to pay 250€ for this anyway), your best bet is to rent a car. There's a good range of options, including Japanese staples Toyota and Nissan rent a car, that would cost you about 80€ with a full insurance, ETC card (always a good choice if you're planning to use Japanese highways) and different place return surcharge.
Last but not least, the quarantine. During our 14 days self-isolation, we weren't called, visited or otherwise checked upon a single time. You're just supposed to be obedient in Japan, no other option.