From having a five-point lead this time last week Ducati rider Bagnaia dropped 23 points behind Martin after a disastrous weekend in Spain which culminated with the ugly accident with Alex Marquez that ended both their races.
The Italian was livid after the crash, claiming that Marquez deliberately ran him off the track and then insulted him once confronted, while Marquez insisted that he would have avoided contact but that Bagnaia made it impossible.
But in Thursday's pre-race press conference Bagnaia apologised to Marquez for the vehemence of his reaction, which he put down to being "very angry after what happened".
"I didn't want to say that he made me crash on purpose, his defence was a bit aggressive but that is normal when you're fighting for podium positions," said Bagnaia.
Marquez told Sky Sport in Italy that the pair had since spoken privately and the matter was now closed.
Just like last year, when he recovered from a huge crash at the Catalunya GP to compete at Misano, Bagnaia will race through the pain on home soil.
"I'm not at my 100 percent, I feel a lot of pain on the shoulder, over the collar bone and neck," added Bagnaia.
"I don't feel like I can move my body as I want... the impact was very huge, 170 kilos were on my shoulder and the hit on the ground was quite huge. Luckily I didn't get any broken bones but the muscles and ligaments are suffering a bit."
The crash, and the elder Marquez, Marc, winning his first GP in three years, blasted wide open the title race, with four riders now in contention and eight races remaining in the season.
Marquez's 'extra boost'
Six-time MotoGP champion Marc Marquez jumped up to third, one point above Enea Bastianini, in the standings after a perfect weekend on his home track last time out, winning both the sprint and the GP.
The 31-year-old, who rides for Ducati satellite team Gresini, is 70 points behind countryman and Pramac rider Martin who has not won a race since May's French MotoGP.
A seventh MotoGP crown would be an incredible feat for Marc Marquez who has had to deal with surgery on a broken arm, multiple crashes and a diagnosis of diplopia, or double vision, over the past few seasons.
"We need to use that extra boost, that extra confidence to continue, to keep going," he said.
"After everything that has happened in my life and in my body, I have to work double, I have to be often with the physio, but it's the way to do if I want to continue in the top level. I'm ready to do it."
Martin won at Misano Adriatico last year and has been knocking on the door recently, finishing second in the sprint and race at four of the last five GPs.
It's been that level of consistency that has allowed Martin to take command of the championship despite only winning two races and one sprint all season.
Bagnaia, who has seven GP wins and three sprint wins under his belt this season, will have some help in the shape of big home support as he bids to reclaim the summit.
This race weekend is the first of two in a row at the Marco Simoncelli circuit, as the track is being used later in September for the Emilia Romagna GP which replaces the cancelled race in Kazakhstan.
