How to research controversial history?

I suggest that you do no real research and just make stuff up. When a historian refutes your claim, refute the historian by showing how his past work on this issue has been one sided. When a non-biased historian refutes you, demand he propose an alternative interpretation. When he has done this, you have thus tricked him into doing the research you set out to accomplish while you personal didn't have to do any real work.

Your question seems more oriented towards recent history than ancient history, so suggesting something for recent history: Follow the money. In most if not all armed conflicts, there are some entities making a killing in monetary terms or terms of political power or possession over material wealth (example: mines), who have a solid incentive to make that conflict carry on or spiral out of control and who might even commit actions to ensure that conflict resolution doesn't happen. And, in some cases, who might even mastermind the conflict-sparking incident to begin with. Qui bono : Who ultimately benefited from the events that took place?

One prime example : terrorist attacks that help the ruling regime divert attention away from their own shortcomings and which galvanize loyalty for the leader of that regime, which push the people into approving undemocratic legislations, decisions which otherwise would never have been accepted. Following which, the side that the terrorists were claiming to have attacked on behalf of, gets clobbered mercilessly and ends up in a much worse state, and the resources that were under their domain are now property of the other. With these kinds of events repeating regularly and with a fairly logical and predictable sorry outcome for the side whom the terrorists represent, it's worth asking if those terrorists were genuinely representing them at all, or were they acting at the behest of the leadership or behind-the-curtain controllers of the aggravated side to justify the next actions that would otherwise never have been approved.

So, here it can become vital to trace the sources of funding involved in the incidents, who is supplying the non-state actors with arms, logistics, who allowed them to get within striking range, which safeguards that would have prevented the attacks failed and were they deliberately failed, did the people in charge at the time get punished for their failure to thwart the attack, etc.

You should consider looking at alternative sources that are not biased as part of your research. For example, the United Nations issues reports that provide a generally unbiased view of situations going on in different countries throughout the world. Usually their reports will provide a fairly accurate view of both sides of the events, and then it is up to the reader to decide whether one side has a distinct moral advantage over the other. There are other organizations as well, such as Amnesty International, that do the same thing from a different perspective and for a different reason.

If the events you are researching extend back beyond the emergence of these types of organizations, then look for sources of information that originated outside your region of interest. For example, information from Jewish trade merchants may provide a generally unbiased view of both sides of the Crusades.

Having said all this, you should not completely discount or ignore the differing opinions within the region you are researching. Each side will certainly paint a picture that favors their viewpoints, but those are valid for providing perspective. Often it is up to the researcher to develop an opinion as to which side is right, but it is better if you can say that you have truly explored both perspectives. Also, sometimes you just have to provide both perspectives and let your intended audience come to their own conclusions.

Try to go back to primary source and archaeological evidences. Are there mass graves? What about population movement? What do statistics have to say about the population, economy, and whatnot?

You can look at the documents and narratives's authors and find out inconsistencies within them or evidence of forgeries/lies -- note that lack of such is not necessarily proof of facts. This may require investigative work on the ground.

The hard thing is not to cherry pick yourself: Please be aware of your own agenda and bias.

Another 3 advices to add to Sardathrion's:

1. Try not to let emotions affect you into mistaking incidents for trends (one such example from History SE was when someone described US involvement in Vietnam as being a pattern of massacres. While Mai Lai is indeed horrific, it's (given the scale) a minor blip that serves to prove the opposite trend (out of 1million+ served, 50 soldiers participated) in dispassionate analysis.

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2. Be careful about logical fallacies.

   Among the most common encountered in discourse about history is confusing causation and correlation.

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3. Be VERY VERY careful about semantic and other word games that biased parties are wont to use. To give 2 types:

   • Using words outside the accepted definitions to tinge the events.

     To use a very controversial example from recent history, look at accusations of G.W.Bush "lying" about weapons of mass destruction in Iraq. If you carefully analyze the claim, "lying" means stating something that one knows NOT to be true, yet there are no documents/witness accounts to prove that Bush White House knew that there were no WMDs prior to Iraq War. They may have lied about their degree of confidence, but they didn't have anywhere near conclusive proof of lack of WMDs.

     A common case of this is to intentionally switch around "murder" and "kill" verbs (the former 100% implies premeditated intent to kill).

   • Another, much more problematic game-wording, is playing with linguistics to prove historical facts/connections from isolated word root similarities etc...

     One less known example is modern Russian revisionist history which contains some fairly outlandish claims about pre-900s Russian tribes based on fancy playing with word roots to prove that certain historical references were about russians/slavs where they are historically accepted as being totally unrelated (It's been a while so I don't have any links to specifics, sorry).

     Another example is the Israeli-Palestinian conflict, where people claim somehow that modern Palestinians have a historical claim to the area stronger than the Israelis because their name derives from Philistines. However, archaeological (and some other, such as linguistic) evidence points to Philistines being of Greek-originated Mycenaean culture, and therefore not of Semitic origins like Arabs who comprise most of Palestinians. The name coincidence was due to geographical naming convention for the area.