It is hard to disagree with the jury’s guilty verdict against Jose Padilla, the accused, but never formally charged, dirty bomber. But it would be a mistake to see it as a vindication for the Bush administration’s serial abuse of the American legal system in the name of fighting terrorism.

On the way to this verdict, the government repeatedly trampled on the Constitution, and its prosecution of Mr. Padilla was so cynical and inept that the crime he was convicted of — conspiracy to commit terrorism overseas — bears no relation to the ambitious plot to wreak mass destruction inside the United States, which the Justice Department first loudly proclaimed. Even with the guilty verdict, this conviction remains a shining example of how not to prosecute terrorism cases.

When Mr. Padilla was arrested in 2002, the government said he was an Al Qaeda operative who had plotted to detonate a radioactive dirty bomb inside the United States. Mr. Padilla, who is an American citizen, should have been charged as a criminal and put on trial in a civilian court. Instead, President Bush declared him an “enemy combatant” and kept him in a Navy brig for more than three years.

The administration’s insistence that it had the right to hold Mr. Padilla indefinitely — simply on the president’s word — was its first outrageous act in the case, but hardly its last. Mr. Padilla was kept in a small isolation cell, and when he left that cell he was blindfolded and his ears were covered. He was denied access to a lawyer even when he was being questioned.