Ok, this is my opinion on the 2015 events.
1. Argentina. Where it all started. Marquez thinks Rossi took him out of the race intentionally. This was confirmed to Rossi by Alzamora. Rossi is on record saying this, which Alzamora did not deny. Alzamora also said that Marquez blamed the foul play from Rossi for losing the championship.
Personally, I doubt you can calculate a move like that to deliberately hit someone behind you without you risking to go down as well. It's unlikely, although Rossi for sure did not do anything to avoid contact as he had the good position, and Marquez had just rammed him and nearly took him out in the previous corner, so things were "hot". Marquez put himself in a very vulnerable position there, far too close. So racing incident IMO.
2. Assen. The last chicane "passing" attempt by Marquez was revenge from Argentina. I believe his intention was to take Rossi out. If you look at the slo mo replay you see his bike is headed towards Rossi, not towards the corner, Capirossi-Harada-1998 style. The Italian was probably expecting it and was quick to go straight through the chicane, the only option he had. Even Marquez himself had to go off track. This infuriated Marquez even more. His denial of any wrongdoing was just a defence mechanism to come across as the "victim". The footage is crystal clear.
3. Philip Island. Marquez and his Honda were the strongest pair at this point and he saw the opportunity to take revenge from Rossi again by interfering in the title fight if he could. After the seagull incident put Lorenzo in the lead, Marquez let him go and held up Rossi and Iannone to help Lorenzo build a gap. His objective was to make Lorenzo finish behind Rossi, and was hoping to manage this without conceding the race win as he had such a massive pace advantage. So he held those two up to about lap 13, then took off and overtook Lorenzo in about 2 laps, hoping the job was done. However, Rossi's and Iannone's race pace that day was faster than Lorenzo's and, even though they were fighting each other, they quickly caught up with the Spaniard. When Marquez saw this, he let himself be passed by Lorenzo and continued to hold the Italians up. He now knew how quickly he would catch Lorenzo again, so he waited until the end to go after him again, hoping to win the race and let Lorenzo take some points off Rossi. It worked. Without Marquez intervention, Rossi would have finished ahead of Lorenzo, and his points lead would have increased by at least 3 points (rather than decrease by 7 points as it happened).
What evidence is there to support this? The lap time patterns, the timing of his very unusual and sharp pace changes, the body language of Marquez' riding, when and where he went wide to slow down, Rossi's and Iannone's comments. If Marquez had raced to win that day, he'd have won by 10 seconds. Marquez said that overheating issues in his tyres made him have erratic lap times and rhythm, but this would have resulted in more gradual changes, it's not consistent with the magnitude and timing of the anomalies in his lap times.
4. After Philip Island. Rossi did not fully realised what Marquez was doing until he watched the race and looked at the lap times. He mentioned it to Yamaha and Dorna, but they could not do anything it could not be proven beyond doubt and it wasn't technically against the rules. However, he felt he had to do "something", and he chose to make it public. Marquez obviously denied this as he'd do in any case.
5. Sepang. Marquez played the offended part and somehow felt entitled to disrupt Rossi's race. Imagine you realise your wife had an affair in the past, you tell her you know, and she goes all offended and does it again in response! It's as mad as that, but some people still justify it.
So yes, Marquez again had more than enough pace to race Pedrosa but chose to wait for Rossi, this time completely unashamedly, letting Lorenzo past by "going wide" at exactly the right time. Then he amused himself by harassing Rossi, a guy with nothing to lose vs a title contender, very fair way to take revenge isn't it? What a gentleman. What could Rossi do? Obviously couldn't get away against the fastest rider that day. He did what he did, went wide, slowed down, a bit like "WTF are you doing" moment. Rossi did NOT take Marquez off the track. Rossi did NOT kick him or made deliberate contact. Marquez turned in and accelerated while Rossi was still side by side, which caused the contact. Rossi's foot came off the peg briefly, and the movement of putting it back in place is what looks like the kick, which the media exploited to no end for all those who were listening.
5. After Sepang. Dorna was under pressure to penalise Rossi because of what it looked like, more than because of what actually happened. Rossi shouldn't have gone wide and created that "situation", but what could he do? It was unprecedented. Dorna's attitude was to try to deny any race fixing agendas and keep the image of the sport clean in the media. The Dorna-friendly press, most of it, followed suit.
6. Valencia. Marquez finished the job by escorting Lorenzo to the win. He din't try to overtake once. It was very embarrasing in the last few laps when Lorenzo dropped the pace considerably due to tyre wear, and Marquez looked like he didn't know how to avoid overtaking him. Pedrosa, who was 3 seconds behind a few laps before quickly caught up with them and tried to pass Marquez, who suddenly showed his characteristic aggressive riding only to keep his team mate behind. If Lorenzo had been third, Rossi would have won the championship, regardless of the events in PI and his penalty for Sepang. After the race, Lorenzo is on record publicly thanking Marquez for helping to keep the title in Spain (!!!).
So that's the story that makes most sense to me. It's consistent with the observations and attitudes we've seen on and off the track, but it might not be the only possibility, simply the most likely to me. You may argue about Argentina, did Marquez have any real reason to take revenge? etc. But denying what Rossi said flat out with any further inquiry is only for those with an agenda to do so.