@Warilized I am going to assume, he was expelled. If you remember correctly, the guardian in the introduction mentioned on how the people who fail would not be killed BUT instead taking to another departments. Since the 6 main clans only needed to get rid of him [with his death of public destitution] , they make a public example of him. Of course, He probably mentioned to his family and his children's family mentioned this thru their generations. Probably a branch of his family in the future waited until the time travel was perfected. We have to remember that if in this story, time travel was discovered, it means that it would have still a long time go before it could be used for the purpose of going thru time and space and was not allowed for everybody.
In the very beginning of the story, it was mentioned that martial arts was then learned thru generations and only the big clans were able to dominate the people. I would say it is a foreshadow to what the future it would be [even if the author never tried to mention it ever again or maybe give us room to see another clan with similar experience to our MC or others would come]. Now, we know that his descendant knew martial arts and got a very advance technology. This tell us that his children got a huge grudge against the big clans. They probably were insulted and even if the future is sort of different, the main branch still remember and they are the underdogs of the future powerhouses. They used those powerhouses to still take advantage and use our MC's descendants as their toy.
It was probably once in a life time chance. This is why even the descendant said, they are almost here [or something like that] and just injected him and left. That way he could get rid of them and lost track of where exactly he was. If the descendant kept moving, that would mean that they wouldn't suspect his ancestor was there and just keep looking for him. In the meanwhile that would change his timeline and he would vanish or like in the movie [frequency] events in the future up to his timeline [of the descendant] things would change and the moment he came back to the future [the descendant present], he would be someone who was in a better social status. Remember the descendant even said, with a grin, to give them a better future this time around.
If you haven't watched the movie frequency, I would suggest you to watch it. It is a good movie and would give you an idea of what I am talking about.