A non-finish at Le Mans opened up the title race, but the defining moment of the season came at Catalunya with the events of the race and aftermath casting a shadow over the middle stages of the championship.
Marquez had saved a crash on the Suter in the closing stages of the grand prix only to then pull his bike across the track collide with adversary Espargaro, who had dived for a gap on the inside of the track. Espargaro fell heavily while Marquez, who said he hadn't seen him, took third.
More drama was to follow when a time penalty imposed by Race Direction was almost immediately overturned, causing weeks of legal wrangling as the Pons team took the result to an FIM hearing. Marquez ultimately kept his points and always maintained that he had not been aware Espargaro was there.
The Pons Tuenti HP 40 rider then responded with a win at Silverstone, but Marquez bounced back with convincing victories at Assen and the Sachsenring circuit.
A disappointing fifth place in Mugello, his worst race finish of 2012, was followed by pure dominance when the paddock reached Indianapolis, the new chassis from testing proving to be a successful addition from Suter.
Victory in Brno over Luthi by a narrow margin while Espargaro was third, despite being penalised for overtaking under yellow flags, kept the battle tight between the pair, only for them to again be in each other's company all the way to the line at Misano, with Marquez coming out on top.
Heading to Aragon with a healthy 53-point lead Marquez started the weekend with his worst qualifying performance of the season only to work his way up to second as Espargaro won a thrilling four-way battle to take his first victory since the British Grand Prix and began to chip away at the points deficit.
Motegi was the scene of Marquez's zero-to-hero moment. After not putting the bike in gear on the line and dropping to the back of the field whilst being lucky to not to be hit he then stormed to the front of the pack after just an handful of laps and stood firm for an incredible race win.
There was a mathematical opportunity for the Spanish youngster to be crowned in Malaysia but Marquez lost the front, falling from a title winning position when under pressure from Andrea Iannone.
Espargaro's eleventh as he struggled in the wet was enough to keep his title aspirations alive for one more week, where his win of over sixteen seconds was impressive but still not enough to deny Marquez his second career title.
Reflecting on the championship win Marquez declared his title to be "an incredible feeling, a dream.”