McLaren knew from early on in the Malaysian Grand Prix weekend that it was going to be difficult to beat Ferrari on pace, and Lewis Hamilton's quickest lap on Friday afternoon was not representative of the comparative speed of the two cars on long runs. The important thing as far as the race was concerned was to secure the second row and not have a BMW or other unwelcome interloper in the way, and initially, McLaren did just that.
The surprise, certainly to the team, was that Heikki Kovalainen was also ahead. In only his second race alongside Hamilton, he made a point by out-qualifying the Briton, and did it with an extra lap's worth of fuel in the tank, as the race was to demonstrate.
Hamilton admitted he had a bad Saturday, and things just did not come together for him, especially when it mattered on the soft tyre.