While in port, the captain of James Adger began the legal questions that would be used in the Trent Affair by loudly speaking of his mission while intoxicated on brandy.

At Charleston, smooth teamwork was the key to success, and James Adger was unusually adept in cooperating with other ships in the area to assure the effectiveness of the blockade.

She assisted Keystone State and Flag in driving off and pursuing her old adversary Nashville — now a blockade runner named Thomas L. Wragg — trying to slip into Charleston.

James Adger sailed for Baltimore on 19 September for repairs and departed for the South on 31 December touching at Hampton Roads on 2 January 1863 to take monitor Montauk in tow before proceeding to Beaufort and Port Royal in preparation for an attack on Charleston.

On 2 April, the veteran ship became flagship for Rear Admiral Du Pont while he supervised final preparations for his powerful monitor attack upon Charleston.

She arrived Philadelphia 25 June but immediately after coaling sailed in pursuit of Confederate commerce railer CSS Tacony, then operating against Union merchantmen far up the East Coast.

Moreover, a package of documents thrown overboard before the capture, when plucked out of the sea, divulged information so important to the South that Cornubia's captain lamented, "though the Cornubia is a small vessel the Confederate Government could better have afforded to lose almost any other..." The next morning, James Adger took Confederate steamer Robert E. Lee coming into Wilmington from Bermuda with a cargo of arms and Army clothing sorely needed by Lee's soldiers.

Schooner Ella, approaching Wilmington with a cargo of salt and yard goods from Nassau, Bahamas, was James Adger's next victim, surrendering on 26 November.

When the ship's long postponed repairs could be delayed no longer, James Adger sailed north and decommissioned at Philadelphia on 28 December for the necessary yard work.