Macarthur, and a special verdict was found. King referred Marshall's allegations to the court, but they would not inquire into them. King re-convened the court, and they adhered to their previous determination. King remitted the fine and imprisonment, conditionally on Marshall's delivering himself up to the Secretary of State within fourteen days of arriving in England, to abide by such directions as might be there given. The decision of the Secretary of State was not received until late in 1803. It stated that King was misled in re-convening the court, which was justified in its conduct. Though the sentence was confirmed, yet "as the period of Lieut. Marshall's imprisonment has expired, and as he has complied with the terms of his recognizance, His Majesty has been pleased to consent that the fine imposed upon him shall be remitted."
The officers were in such ill-humour at Marshall's departure that many of them resolved to insult the Governor. Colonel Paterson showed no favour to their resolution. Macarthur, ever impetuous, quarrelled with Paterson, who "exacted satisfaction" in a duel in which Paterson was dangerously wounded (Sept. 1801). Macarthur and his second, Piper, and McKellar, the second of Paterson, were put under military arrest until the result of the wound might be known. When Paterson's life was out of danger Macarthur was ordered to embark for service at Norfolk Island. On the 21st Sept. it was ordered that the arrested officers should be released on bail, giving security to appear before the Criminal Court in case of Paterson's death from the wound. All four were to enter into recognizances to keep the peace. Paterson, Piper, and McKellar entered into recognizances, but Macarthur refused to give security, would not quit his arrest, and demanded a court-martial. Another General Order (23rd Sept.) declared:
"Notwithstanding this defiance of the civil law and the king's authority, the Governor foregoes the line his duty points out, by committing him to the public gaol until he gives the sureties required, on account and in consideration of his family. In consequence of this officer's refusal to come out of arrest, and give security for his future peaceable behaviour, the indulgence the Governor allowed him, at his own request, of going about Parramatta, is for the preservation of the king's peace to be withdrawn, and he is to be placed under a close arrest. His Majesty's service requires that Captain John Macarthur do prepare himself to embark for England in the arrest he has thought proper to continue himself under."