i find it very confusing
Stories involving time travelling usually are.
(Spoiler)
Basically there is a boy who goes to spend time with a father who he barely knows since his parents divorced when he was young. During that awkward period he manages to time travel to the past to meet his father who was 14 years at the time. They spend time with each other and fall in love. The father doesn't know he is his child but the latter obviously knows and still does the unthinkable with the father. So when the son returns to his original time period he wants to continue their love but by that time the father knows that they both have committed a grave taboo. Some pretty deep feeling get involved and Ryou tries to respect his father's wishes and forget about their love but in the end... bam! (yaoi style) they get together.
That's the main story. The issue of Ryou burying and digging up various things from under the stone in the yard hold significant value in allowing the events of the time travel to occur. However if you don't get it it's not gonna affect the overall understanding of the plot.
This was a beautifully written story but in retrospect I still can't get over the fact that this is completely wrong in so many ways. It was a decision for the characters to say fuck it and let's stay together for happiness but reality is much harsher than this prettily wrapped ideal of a conclusion.