Eagan was commissioned as a 1st lieutenant in the 1st Washington Territory Infantry Regiment on June 21, 1862, during the American Civil War.

He received a retroactive brevet (honorary promotion) to the rank of captain on February 27, 1890, for "gallant service in action against hostile Indians in the Lava Beds, California on April 17, 1873".

[2] General Eagan took this statement as a personal insult and openly denounced Miles as a liar when called to testify on January 12, 1899.

[3] As a result of Eagan's aspersions towards Miles, who had a long and distinguished military career as well as being a recipient of the Medal of Honor, he was quickly court-martialed for "conduct unbecoming an officer and a gentleman" and was suspended from duty until he retired on December 6, 1900.

[5] He was also expelled from membership in the District of Columbia Commandery of the Military Order of the Loyal Legion of the United States.

After a protracted struggle with other speculators, in May 1902, Eagan won a case in the Mexican Federal Court which granted him ownership of 2,500,000 acres in western Mexico.