Here is the discussion in question. This should not be viewed as a schollarly source, it's really just a conversation. (As a personal note the entire discourse is an entertaining read, regardless of its informativeness.)
I'm curious to hear /r/AskHistorian's interpretation of Chomsky's theory/opinion/understanding that Japan could easily justify its actions in World War II as being for the "greater good." Obviously this is something that my country, the United States, excels at ("We'll be greeted as liberators!") but I never hear about the justifications from the other side of the fight.
What noble, sincere intentions did the Japanese believe they had when entering World War II; and was there any evidence to reinforce those beliefs?
The "sincere intentions" of the Japanese Imperialists were similar to those of any other expansionist imperialist power. The Imperialists honestly believed, or convinced themselves they believed, that expanding the Japanese demesne would be good for both the Japanese people and those they were conquering. The propaganda term coined for this was the Greater East Asia Co-Prosperity Sphere, implying that both the conquerors and the conquered would benefit.
One frequent "sincere intention" is that the imperial power is alleged to spread "civilization" or perhaps "liberate" the populace from an extant government deemed by the imperialist power to be oppressive or tyrannical.
More broadly, Chomsky is making a point that history seldom looks kindly on the "good intentions" of conquerors. While we may read paeans to the Pax Romana, civilizing Europe, we also know of the millions of people killed and enslaved to enforce it.