"The relationship with Valentino was really good until Thursday (before) Malaysia," the Spaniard told CNN. "I think there he created so much more of what was not natural, not good for motorcycling."
Rossi missed out on the 2015 title to Spaniard Jorge Lorenzo, and accused Marquez of helping his compatriot to the crown.
The Italian was penalized at October's Malaysia MotoGP after forcing Marquez wide and appearing to kick out at his bike, causing him to crash. Rossi began the final race in Valencia from the back of the grid, eventually finishing in fourth -- short of the points needed for his 10th title.
The 22-year-old Marquez desperately wanted to win in Valencia, partly to prove Rossi wrong.
"The problem is that too many people start to speak about the situation," said the Spaniard.
"(When we arrived) in Valencia, I say 'Please we need to win the race because if not ... he will complain.'"
In the end, he said, Lorenzo was simply too fast.
"Lorenzo did the fastest lap, the record of the circuit, the record of the total laps ... I couldn't pass him, I couldn't win; but you know for me the target was to win the race and that was the best way to finish the season," added Marquez.
After all those shenanigans the Repsol Honda rider says he wants a fresh start with Rossi.
"I already said in Valencia to Valentino, 'My hand is here,' and I want the best for motorcycling, and I think the best thing is to be in a good relationship with him."
But not quite yet perhaps -- Marquez believes the right time for a reconciliation may come when Rossi wins again.
"At that moment (in Valencia) he had just lost the championship, and he was really worn.
"I understand the situation, so I don't want to think a lot about what he said, but I hope that 2016 will be a new season, a new relationship and (we) try to forget all these things."
"When he wins we can discuss and we can speak," added Marquez.
Marquez was speaking at a training camp for junior motorcycle riders -- part of Laps for Life 93
, a social initiative the rider is spearheading.
Twenty young riders between the ages of nine and 13, from Spain, Italy, the UK, the Netherlands and Brazil were selected by Marquez to take part in the camp.
"The way that you speak, the way that you ride the bike, the way you eat something, they are looking all the time," he explained.
"You must be right at these thing because you know what you will do they will copy."
Before the Valencia race, MotoGP bosses urged riders to carefully consider their actions both on and off track in the wake of the drama between Marquez and Rossi. Marquez clearly welcomed the attitude of the youngsters at the camp.
"On the track they can overtake, they are fast, they are pushing the limit; but look now they are here playing football, playing between them, and this is the real spirit of playing motorbikes -- the real relationship.
"They can fight on the track, but when they take off the helmet they are friends."