Belligerent opposition to European and American influence erupted into open conflict when the Emperor Kōmei, breaking with centuries of imperial tradition, began to take an active role in matters of state and issued on March 11 and April 11, 1863, his "Order to expel barbarians" (攘夷実行の勅命 – Jōi jikkō no chokumei).

The Chōshū clan, under the daimyō Mōri Takachika, began to take action to expel all foreigners after the deadline of the 10th day of the 5th month, according to the traditional Japanese calendar.

McDougal wrote a letter to the Secretary of the Navy, Gideon Welles, dated June 12, 1863, stating, "General opinion is that the government of Japan is on the eve of revolution, the principal object of which is the expulsion of foreigners."

The U.S. merchant steamer SS Pembroke, under Captain Simon Cooper, was riding at anchor outside Shimonoseki Strait when it was intercepted and fired upon by two European-built warships belonging to the rebel forces.

The next day, the French naval dispatch steamer Kien Chan was also riding at anchor outside the strait, when rebel Japanese artillery atop the bluffs surrounding Shimonoseki opened fire on her.

Her skipper, Captain François de Casembroot, was convinced that Lord Mōri Takachika would not dare fire on his vessel due to the strength of his ship and longstanding relations between the Netherlands and Japan.

De Casembroot returned fire and ran the rebel gauntlet at full speed, fearful of endangering the life of the Dutch Consul General, who was on board.

In the morning of July 16, 1863, under sanction by Minister Pruyn, in an apparent swift response to the attack on the Pembroke, the U.S. frigate USS Wyoming, under Captain McDougal, sailed into the strait and single-handedly engaged the U.S.-built but poorly manned local fleet for almost two hours before withdrawing.

Despite retaliatory action from the treaty powers, another attack occurred in July 1864 when the rebel forces fired upon the U.S. steamer Monitor after she entered a harbor for coal and water.

On August 17, 1864, a squadron consisting of nine British (Euryalus, Conqueror, Tartar, Leopard, Barrosa, Perseus, Argus, Coquette, and Bouncer), four Dutch (Djambi, Metalen-Kruis, Medusa, and Amsterdam), and three French warships (Tancrède, Sémiramis, and Dupleix), together with 2,000 soldiers, marines and sailors, all under the command of Admiral Sir Augustus Leopold Kuper of the Royal Navy, steamed out of Yokohama to open Shimonoseki Strait.

Unable to match the firepower of the international fleet, and amid mounting casualties, Takasugi Shinsaku negotiated peace with the four Western powers and Chōshū forces finally surrendered two days later on September 8, 1864.

The stringent accord, drawn up in the wake of the ceasefire and negotiated by U.S. Minister Pruyn, included an indemnity of $3,000,000 from the Japanese, an amount equivalent to the cost of about 30 steamships at that time.

Closely resembling the series of little conflicts fought by the European powers in Asia, Africa and elsewhere during the nineteenth century, the troubles in Japan seemed to exemplify their gunboat diplomacy, a prevalent tool in imperialism.

Bitter resentment against foreign influence made the Chōshū clan feel justified in engaging in acts of military provocation in defiance of their own government.

[citation needed] While the battles of Shimonoseki Strait were mere footnotes in the histories of the European powers, an interesting aspect of the affair was the resourcefulness displayed by the Japanese.