The area to the north of the pueblo of San Luis Obispo was under the control of Alta California's Commandante José Castro with headquarters near Monterey, the traditional capital and, significantly, the location of the Customhouse.

In his decree dated November 6 he wrote: "Therefore conciliating my duty [to enforce the orders from Mexico] with of the sentiment of hospitality which distinguishes the Mexicans, and considering that most of said expedition is composed of families and industrious people, I have deemed it best to permit them, provisionally, to remain in the department" with the conditions that they obey all laws, apply within three months for a license to settle, and promise to depart if that license was not granted.

As a military officer he could face court-martial for violating the Neutrality Act of 1794 that made it illegal for an American to wage war against another country at peace with the United States.

[23] U.S. Consul Thomas O. Larkin, concerned about the increasing possibility of war, sent a request to Commodore John D. Sloat of U.S. Navy's Pacific Squadron, for a warship to protect U.S. citizens and interests in Alta California.

After receiving information about Frémont's returning to California, Consul Larkin and Portsmouth's captain John Berrien Montgomery decided the ship should move into the San Francisco Bay.

[25] William B. Ide, a future leader of the Revolt, writes of receiving an unsigned written message on June 8, 1846: "Notice is hereby given, that a large body of armed Spaniards on horseback, amounting to 250 men, have been seen on their way to the Sacramento Valley, destroying crops and burning houses, and driving off the cattle.

Fremont invites every freeman in the valley to come to his camp at the Butts [sic], immediately; and he hopes to stay the enemy and put a stop to his" – (Here the sheet was folded and worn in-two, and no more is found).

[28] Some of the group who had been meeting with Frémont departed from his camp and, on June 10, 1846, captured a herd of 170 Mexican government-owned horses being moved by Californio soldiers from San Rafael and Sonoma to the Californian Commandante General, José Castro, in Santa Clara.

[31][32] Historian George Tays has cautioned "The description of the men, their actions just prior and subsequent to the taking of Sonoma, are as varied as the number of authors.

"[33] Historian H. H. Bancroft has written that Frémont "instigated and planned" the horse raid, and incited the American settlers indirectly and "guardedly" to revolt.

He also solemnly declares his object to be First, to defend himself and companions in arms who were invited to this country by a promise of Lands on which to settle themselves and families who were also promised a "republican government," who, when having arrived in California were denied even the privilege of buying or renting Lands of their friends, who instead of being allowed to participate in or being protected by a "Republican Government" were oppressed by a "Military Despotism," who were even threatened, by "Proclamation" from the Chief Officer of the aforesaid Despotism, with extermination if they would not depart out of the Country, leaving all of their property, their arms and beasts of burden, and thus deprived of the means of flight or defense.

To overthrow a Government which has seized upon the property of the Missions for its individual aggrandizement; which has ruined and shamefully oppressed the laboring people of California, by their enormous exactions on goods imported into this country; is the determined purpose of the brave men who are associated under his command.

He also solemnly declares his object in the Second place to be to invite all peaceable and good Citizens of California who are friendly to the maintenance of good order and equal rights (and I do hereby invite them to repair to my camp at Sonoma without delay) to assist us in establishing and perpetuating a "Republican Government" which shall secure to all: civil and religious liberty; which shall detect and punish crime; which shall encourage industry, virtue and literature; which shall leave unshackled by Fetters, Commerce, Agriculture, and Mechanism.

He further declares that he relies upon the rectitude of our intentions; the favor of Heaven and the bravery of those who are bound to and associated with him, by the principle of self preservation; by the love of truth; and by the hatred of tyranny for his hopes of success.

That its Citizens are its Guardians, its officers are its Servants, and its Glory their reward.A major problem for the Bears in Sonoma was the lack of sufficient gunpowder to defend against the expected Mexican attack.

William Todd was dispatched on Monday the fifteenth, with a letter[notes 2] to be delivered to the USS Portsmouth telling of the events in Sonoma and describing themselves as "fellow country men".

[43] Todd, José de Rosa (the messenger Vallejo sent to Montgomery), and U.S. Navy Lieutenant John S. Misroon returned to Sonoma in the Portsmouth's launch the morning of the 16th.

[46] Frémont's "field-lieutenant" Merritt returned to Sacramento (known as New Helvetia at the time, so named by the Swiss John Sutter) on June 16 with his prisoners and recounted the events in Sonoma.

[47] Frémont recounts in his memoirs, "Affairs had now assumed a critical aspect and I presently saw that the time had come when it was unsafe to leave events to mature under unfriendly, or mistaken, direction … I knew the facts of the situation.

[51][52] Word of the taking of the government horses, the capture of Sonoma, and the imprisonment of the Mexican officers at Sutter's Fort soon reached Commandante General José Castro at his headquarters in Santa Clara.

Ford also learned that William Todd and his companion had been captured by the Californio irregulars led by Juan Padilla and José Ramón Carrillo.

Militiamen from south of the Bay, led by Mexican Captain Joaquin de la Torre, had joined with Padilla's irregulars and now numbered about seventy.

Frémont would say in his memoirs that he wrote a letter of resignation from the Army and sent it to his father-in-law Thomas Hart Benton in case the government should wish to disavow his action.

[61][62] Late the same afternoon as the killings, a scouting party intercepted a letter indicating that Torre intended to attack Sonoma the following morning.

He arrived back at the old mission within twenty-four hours of leaving but during that period Torre and his men had time to escape to San Pablo via boat.

[64] On July 1, Frémont and twelve men convinced Captain William Phelps to ferry them in the Moscow's launch to the old Spanish fort at the entrance to the Golden Gate.

Frémont and the contingent from San Rafael arrived in time for the fandango held in Salvador Vallejo's big adobe on the corner of the town square.

)[71] Commodore John D. Sloat, commanding the U.S. Navy's Pacific Squadron, had been waiting in Monterey Bay since July 1 or 2 to obtain convincing proof of war.

In 1878, at the request of the Los Angeles Evening Express, William L. Todd (1818–1879) wrote an account of the Bear Flag used at the storming of Sonoma, perhaps the first to be raised.

[80] Todd acknowledged the contributions of other Osos to the flag, including Granville P. Swift, Peter Storm, and Henry L. Ford in an 1878 newspaper article.