Linn was intensely loyal to Texas and the De León colony and was among the first to oppose Antonio López de Santa Anna. He helped unite sentiment against the dictator by writing letters to Stephen F. Austin's colonists. With Plácido Benavides he served in Victoria's Committee of Safety and Correspondence and upon advice from friends in Mexico warned that Gen. Martín Perfecto de Cos would land at Copano as early as July 1835. Benavides, captain of the Victoria militia, and Linn, who had been a captain in the New Orleans militia, helped train the Texan forces amassing at Gonzales after the skirmish there of October 2, 1835. Upon Cos's landing at Copano, Linn and others proposed intercepting the Mexican general on his way to Goliad and San Antonio. Finding small support at Gonzales, however, Linn and Benavides joined a contingent of about fifty men under Benjamin Fort Smith and William H. Jack, who set out to liberate Goliad from Cos's occupation; another Texan force under George M. Collinsworth gained this victory, however, on October 10. On October 8, 1835, Linn became quartermaster of the Texas army, and with James Kerr joined the Goliad garrison, bringing carts, oxen, supplies, and munitions. Linn and Kerr, together with Thomas G. Western, successfully negotiated a treaty of neutrality with local Karankawa Indians on October 29. Two days later Linn served as adviser in Ira Westover's victorious campaign against Fort Lipantitlán on the Nueces River north of San Patricio, a campaign that removed the only remaining link in the Mexican line between Matamoros and San Antonio.
Linn then traveled to San Felipe to represent Victoria in the Consultation of 1835, already in session, which protested Santa Anna's measures and supported the Mexican Constitution of 1824. He also served in the General Council, the provisional government of Texas as a separate Mexican state. In 1836 Linn was elected alcalde of Guadalupe Victoria and in that capacity entertained the Red Rovers and New Orleans Greysqqv on their way to join James W. Fannin's command at Goliad. Linn's wife used their home as a meeting place for the women of Victoria, who molded bullets there for the cause. With José M.J. Carbajal Linn was elected to the Convention of 1836, which declared the independence of Texas from Mexico. The two men did not reach Washington-on-the-Brazos to sign the document, however, because the approach of the Mexican army to Victoria necessitated their return. As army quartermaster, Linn supplied Fannin with twenty yokes of oxen to hasten the commander's retreat from Goliad, but in so doing deprived his family and fellow Victorians of a means of escape. Nevertheless, as alcalde he directed his citizens to retreat to Cox's Point, east of Lavaca Bay, and secured his family in the protection of Fernando De León. During the ensuing occupation of Victoria by José de Urrea's forces, Linn's house was plundered.
Eventually Linn joined Sam Houston near Groce's Retreat. Because Linn's merchant ship had not been captured, Houston sent him to supervise the evacuation of Harrisburg. Under orders from Houston and ad interim president David G. Burnet, Linn then sailed to Galveston Island at his own expense to pick up $3,600 worth of supplies; then, with about fifty men and two cannons, the quartermaster sought Houston and the Texas army. He found them celebrating victory at San Jacinto, where his supplies were the first to reach the Texans after the battle. At the request of President Burnet, Linn interviewed the captured Santa Anna, who knew the alcalde from Victoria. Linn also supplied the first reports of the San Jacinto victory, which were published in the New Orleans Bee and Bulletin. As part of the surrender settlement he provisioned the retreating Mexican army to prevent plundering. Ironically, Linn was arrested as a spy in June 1836 in Harrisburg and upon returning to Victoria was arrested with some members of the De León family as a potential enemy of the Republic of Texas because of supposed sympathies with Mexico. He was soon released.
During the Republic of Texas era, Linn, the last alcalde of Victoria, was elected the town's first mayor, on April 16, 1839. He served in the House of the Second and Third congresses of the Republic of Texas, 1837-39, where he ardently supported the policies of President Houston. After 1836 the port of entry he established at Linnville attracted settlers and promised growth, but it was sacked and burned in the Comanche raid of August 1840 and never rebuilt. In 1842 Linn joined a reconnaissance force to discover the location of the invaders led by Rafael Vásquez and supplied the Texas army with beef. By 1850, at age fifty-two, Linn had $20,000 in property, and the 1860 census listed him as owning seven slaves. He served Victoria again as mayor in 1865 and was a leader in the establishment in 1850 of the San Antonio and Mexican Gulf Railway. He was also a charter member of the Powderhorn, Victoria and Gonzales Railroad Company, which planned a road to bypass Port Lavaca and connect Indianola with Victoria and Gonzales, but was never built. In 1883 he published his memoirs, Reminiscences of Fifty Years in Texas, significant for its account of the revolutionary period. Although these memoirs are Linn's own retrospection, the book was actually ghostwritten by his close friend, the historian Victor Marion Rose. On October 27, 1885, Linn died in the home he had built fifty-six years earlier as a De León colonist.
Among his brothers were Edward, a civil engineer, county surveyor, and Spanish translator in the General Land Office; Henry, a lawyer in New Orleans; and Charles, a doctor who died administering aid in Candela, Coahuila, during a cholera epidemic in 1833. John J. Linn married Margaret C. Daniels of New Orleans in 1833, and among their fourteen children were Charles Carroll, an inspector of hides and animals and a captain in the Fourth Texas Mounted Volunteers; John, Jr., who fought for the Confederacy and died at Brownsville; William F., a druggist and the editor and publisher of the Wharton Spectator; and Edward Daniel, a four-term congressman and three-term senator in the Texas state legislature, editor and publisher of the Victoria Advocate in the 1870s and 1880s, author of his father's lengthy Advocate obituary of October 31, 1885, and a director of the New York, Texas and Mexican Railway Company; in the Advocate building Edward Linn also maintained a small collection of animal fossils now in the Smithsonian Institution in Washington, D.C.
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