Most methodology chapters I read are well-organized, clearly written, and missing an argument. They describe what was done in careful detail — and never quite explain why that was the right thing to do, out of every option available.
Description vs. justification
Description says: I surveyed 240 participants using a five-point Likert scale. Justification says: I used a five-point scale rather than a seven-point one because [specific reason tied to your population or research question].
A methods chapter without justification reads like an instruction manual, not a case — and a committee's job is to test the case.
The question your committee is actually asking
Underneath every methods question in a defense is really one question: why should I trust this choice over the alternatives you didn't take? If your chapter doesn't already answer that, the committee will ask it live — and it's much easier to answer on paper, calmly, than out loud, under questions.
Every methods choice needs a ‘because’ attached to it — or it isn't a choice yet, just a habit.
A simple rewrite test
Go through your methods chapter and find every sentence that describes a choice — sample size, instrument, coding scheme, analysis. For each one, add a clause that starts with “because.” If you can't finish that sentence, that's a gap, not just a stylistic issue.
Where to add the missing argument
You don't need to rewrite the whole chapter. Usually, one paragraph per major methodological choice — addressing the most obvious alternative and why you didn't take it — is enough to shift the chapter from a report into an argument.