Behe covers several sections in detail but here is the overall summary at the end:
The CourtÃ¢â‚¬â„¢s reasoning in section E-4 is premised on: a cramped view of science; the conflation of intelligent design with creationism; the incapacity to distinguish the implications of a theory from the theory itself; a failure to differentiate evolution from Darwinism; and strawman arguments against ID. The Court has accepted the most tendentious and shopworn excuses for Darwinism with great charity and impatiently dismissed arguments for design.
All of that is regrettable, but in the end does not impact the realities of biology, which are not amenable to adjudication. On December 21, 2005, as before, the cell is run by amazingly complex, functional machinery that in any other context would immediately be recognized as designed. On December 21, 2005, as before, there are no non-design explanations for the molecular machinery of life, only wishful speculations and Just-So stories.