For the people who don't get the ending, here's the jist of it as far as I can tell:
The country is suffering extraordinarily from some manner of sickness. Likely some form of the black plague. But, nobody is generally aware of it yet. This was foreshadowed back in the village with the well. The village was convinced that the cultists were oppressing them. In truth, the water in the well was infected. Some nebulous power, be it their goddess or something else, was warning them against drinking it, which was why they were driving people away and calling it "tainted". The villagers thought that the cultists were poisoning people and leaving their bodies out in the middle of the night as a threat. In truth, the dead were those whom were drinking from the well, be it openly or in secret, which is why the little girl is there. The cult was protecting people from a threat they didn't even really understand, and nobody else had even the slightest inkling existed.
While there, the commoner and the slave both drank the water. Or, at the very least, the commoner did. He became a carrier for the disease. On the way, they pick up the cat.
Then, they came across the paranoid villagers burning "witches". They're doing so because they believe "witches" are "cursing" people. The signs of the curse line up with symptoms of plague, showing that the plague has already begun to spread throughout the country.
They try to burn her in their paranoia, but are killed by the swordsman. The swordsman looks over the commoner, but appears to show mercy. The swordsman also reveals the cat belongs to him.
In truth, the commoner is dead. He either succumbed to his wounds, or the plague. Probably the latter, and odds are the swordsman, examining his corpse, recognized symptoms of disease. He then put two and two together with what he had likely been hearing about the witch burnings and the symptoms of the "curse" and realized there's an outbreak. The cat likely also carries it, because its been exposed to them for an entire night. Thus, he kills the cat since it belongs to him and will continue trying to follow him if he doesn't. He lets the slave leave with her master's corpse, be it out of a sense of mercy, or respect for her willingness to fight him to protect others. Either way, because they're no threat to him, and he leaves the country to escape the plague while he still can.
The Slave is either in denial of the commoner's death, or fully aware of it. My money is on the latter, because she too is a carrier of the plague, either from drinking the water or just being in contact with the commoner. Either way, she's surely feeling the symptoms of the plague to some degree. Going off the logic that she's fully aware and not just insane, she returns home to lay the commoner to rest somewhere respectful. The Princess is bewildered by her erratic behavior, but upon realizing the commoner is dead and seeing his limb, she is either horrified and intimidated beyond the ability to act, OR came to realize that he had died to a plague and she had just been exposed. She makes specific note of the fact that the commoner's limb had blackened, and blackened appendages are a symptom of plague.
On the flip side, Slave is fully aware that by returning, she's also exposing everyone there to the plague. In essence, she's getting revenge for the struggles they inflicted upon the pair, which led to her master's death. One way or another, she's taking them down with her.
Her strange personality is due to he upbringing in slavery. She ties the worth of her life to the wellbeing of her master, and now her master is dead. She knows the plague will take her too soon enough, so, wanting to be close to the last person she ever knew who gave her worth, she lays down beside so she can die together with him.
The hammer and the note is likely either just a throwback to the earlier, more comedic tones of the story, or is a warning that if someone comes across her and she seems to be still alive, she needs to be put down because she's a carrier.
Meanwhile, the swordsman is leaving the country, saying it is doomed because he's one of the only ones aware of the full extent of how bad the outbreak has actually gotten even though nobody else is really even aware of it happening at all yet. He also likely predicted that due to her brazen nature, the slave's reaction to finding out her master was dead would be to do exactly what she ended up doing, and by proxy, the royal family, the royal guard, the entire hierarchy of the country, was doomed to infection.
Thus, the story ends on a very bitter note. The heroes are dead one way or another, but everyone who wronged them is already dead as well. They just don't know it yet, and by the time they do, it will be too late. Their suffering as they die from the plague will be multitudes greater than all the torment they ended up putting the main characters through for what ultimately amounted to a bratty outburst from a stuck-up princess. The spoiled brat, in the end, doomed her entire country for the sake of a single insult.