In 1878, he won election as a Democrat to represent Brooklyn in the New York State Assembly.  Flynn was at that time emerging as one of the leading contractors in the area, and soon moved to New York City, where he took an active role in Democratic politics.  The article credited him with convincing Mayor Franklin Edson, a Democrat, to appoint Rollin Squire as commissioner of public works at the end of the mayor's term in December 1884.  It was reported, though, that Flynn and Squire later had a falling out over the latter's association with Republicans and Tammany Hall, the Democratic rival to Flynn's County Democracy machine.  Harper's Weekly estimated that Flynn was worth one to one-and-a-half million dollars in 1886.

The 48-year-old Squire was born in Vermont and attended school in Chester, where he met the future Mayor Edson.  After graduation, Squire moved to Boston to practice law, but spent more time following in his father's footsteps by working as a spiritualist medium.  He displayed his spiritualist talents on a successful tour of Europe, and then returned to Boston, where he became the law partner of W. A. Simmons, and invested in Western mines.  In the early 1880s, he moved to New York City.  In 1885, a bill to enlarge the powers of the commissioner of public works failed to pass the state legislature.

Just over three months after publication of the aforementioned biographical sketches, Harper's Weekly first discussed the alleged improprieties of Squire and Flynn in an August 8 editorial entitled "Tweed Again."  The city's daily press had revealed that in late 1884 Squire wrote a letter asking Flynn to influence the Board of Alderman to approve his appointment as public works commissioner.  In return, Squire promised to send government contracts Flynn's way.  When the bribery became public, the County Democracy immediately expelled Flynn.  

Meanwhile, a state assemblyman from Buffalo named Sheehan steered through the Republican-controlled legislature a bill that removed the mayor and comptroller of New York City from the Aqueduct Commission, and replaced them with non-city residents.  Squire, the commission chairman and its only remaining New York City resident, then named Sheehan, a close ally of Governor Hill, as board secretary.  Governor Hill, a Democrat, was alleged to have had a copy of Squire's letter to Flynn when he signed the bill.  Editor George William Curtis summarized the Aqueduct Commission Act as a swindle by members of both parties against the public.  The editor observed with relief, "The Flynn and Squire exposure has come early, and before a new and complete Tweed system could be organized. But it was the beginning of the same thing."

In the August 21 edition of Harper's Weekly, the lead editorial focused on the Squire-Flynn scandal.  Editor Curtis identified "The Root of the Evil" as the system of political patronage, which made appointment to government office a reward for partisanship and an opportunity for graft, rather than merited service for the public good.  His proposed solution was "to lift municipal politics out of the mire of party" by making public works nonpartisan and managing them on honest business principles.  Two weeks later, Curtis called for the strengthening the mayor's authority, including the removal power.  The same issue reported that Governor Hill had removed Squire from office.