Step One: Assemble the historical records.
Step Two: Apply the principles of the historical method.
Step Three: Come to conclusions based on the data.
Sami and Bassam's Method:
Step One: Figure out, prior to investigation, what they want to believe and what will look best for Islam.
Step Two: Try to find at least some kind of evidence that agrees with the claims they decided to believe prior to any investigation.
Step Three: Throw out or reinterpret all evidence that proves their view false.
To see how Sami reinterprets pretty much everything in the Qur'an and the Hadith concerning violence, just watch our debate here. To see how Bassam does the same thing, consider the following example.
In Ibn Ishaq (Islam's earliest biographical source on the life of Muhammad), we read the following narrative about Muhammad torturing a man to find some treasure:
Kinana b. al-Rabi, who had the custody of the treasure of B. al-Nadir, was brought to the apostle who asked him about it. He denied that he knew where it was. A Jew came to the apostle and said that he had seen Kinana going round a certain ruin every morning early. When the apostle said to Kinana, 'Do you know that if we find you have it I shall kill you?' he said Yes. The apostle gave orders that the ruin was to be excavated and some of the treasure was found. When he asked him about the rest he refused to produce it, so the apostle gave orders to al-Zubayr b. al-Awwam, 'Torture him until you extract what he has,' so he kindled a fire with flint and steel on his chest until he was nearly dead. Then the apostle delivered him to Muhammad b. Maslama and he stuck off his head, in revenge for his brother Mahmud. (Ibn Ishaq, Sirat Rasul Allah, p. 515)
Bassam admits that he was quite disturbed by the implications of this passage, namely, that Muhammad would torture and kill someone over money. Not surprisingly, he used his methodology to reject the facts about his prophet.
Step One: Conclude that Muhammad would never do such a thing.
Step Two: Look for evidence to support this view. (Oops, there is none.)
Step Three: Throw out sources that prove his view wrong.
Thus, Bassam threw out Ibn Ishaq, which non-Muslim historians generally regard as our most accurate source on the life of Muhammad.
Apart from the fact that Bassam threw out an early story about Muhammad with no counter-evidence, there's an additional problem with his approach. As Sam Shamoun's article here proves, most of the story is confirmed in Sunan Abu Dawud (most notably the part about Muhammad having Kinana killed because he didn't tell him where the treasure was).
So here's what we have.
(i) Ibn Ishaq reports a story about Muhammad torturing and killing a man over some money.
(ii) Abu Dawud confirms most of the story.
(iii) There is no evidence that this event never occured.
(iv) Bassam rejects the story, in spite of the evidence, because it makes Muhammad look bad.
This is a methodology we will see again and again as we examine the claims of Sami and Bassam (especially in their amazing reinterpretation of the battle between Aisha's forces and Ali's forces). Sam's article includes another example of Bassam applying the same methodology to rule out another embarrassing story about Muhammad--his decision to divorce one of his (many) wives because she was no longer physically attractive. Stay tuned for more!