Quite Monkeytrousers.
So Dr Wakefield et al observed children with a bowel disorder that they had not seen before. They examined this group of children within the scientific context of the time. The context provided them with information that had been researched by others and themselves over a number of years. None of this science hit the papers, made the public eye or had been considered terribly controversial. The information scientifically shows that measles virus can cause bowel problems, developmental regression, loss of skills, digestive disorders, immune system disorders and so on.
Building on what had been previous established with regards to measles virus plus observing that these children developed their symptoms in the period following exposure to measles virus, it was hardly a huge leap to suggest that this exposure had played a role in the development of the observed and documented symptoms.
The exposure happened to be through vaccination so the paper was destined to piss a lot of people off.
So Dr Wakefield et al who had been trying to meet with the Department of Health for quite some time to discuss their concerning (one would have thought) findings recommend that more research is done ASAP. They do not claim to have shown causation, they say more larger studies need to be done. In the meantime they suggest that it might be prudent to offer single measles vaccine as it does not appear to be implicated.
Ten years on and we are still waiting for the government to commission a study that accurately reproduces, challenges and tests this original early report.
Oddly lots of time and money seem to have been spent on studies that try to disprove claims that were never made in the original report or looking for needles in epidemiological haystacks.