His boat was “Bullet Proof,” but he was not.

In fact, it was Kwame R. Brown’s 38-foot Chris-Craft cabin cruiser — or, more precisely, the home-equity loan taken out to pay for it — that became the hole in the D.C. Council chairman’s political Kevlar.

Federal prosecutors charged Brown (D) on Wednesday with a felony count of bank fraud; he resigned and is expected to plead guilty Friday.

The charge comes precisely five months after Brown’s former council colleague Harry Thomas Jr. (D) pleaded guilty to stealing public funds, and prosecutors remain trained on Mayor Vincent C. Gray’s 2010 campaign after securing felony guilty pleas from two campaign operatives.

But Brown’s demise stands to leave a serious scar on the local body politic.

In the first 37 years of D.C. home rule, no mayor or council member resigned under criminal duress. Now Brown becomes the second to do so in a matter of months.

He is also the first D.C. Council chairman — the city’s second-highest elected office — to resign.

His departure further upsets a political scene that just two years ago appeared to resemble a carefully stacked apple cart, with Brown in a prime spot to assume the mayor’s job.

And now some congressional leaders, for the first time in more than a decade, are seeing an opening to question the city’s locally elected leadership.

“City leaders keep arguing for more autonomy, but it’s hard to get there when so many people keep getting indicted,” said Rep. Jason Chaffetz (R-Utah), a member of the House Government Reform and Oversight Committee, which has jurisdiction over District matters. “This is embarrassing, and the city deserves better.”

Chaffetz added that “by and large, people from outside D.C. don’t view the city leadership very favorably.”

The recent turmoil stands in odd contrast to the city government’s last period of unrest — and congressional intervention — in the early 1990s. Aside from Mayor Marion Barry’s 1990 drug arrest, which resulted in a misdemeanor conviction — the city’s ailments had more to do with rampant mismanagement than with criminal wrongdoing by elected officials.

Today’s investigations into Thomas, Brown and Gray are juxtaposed with stuffed coffers, competent government services, a growing population and a widespread sense that the city is on the upswing. Brown’s alleged offense did not involve misuse of his official position.

Still, plenty in the city are wondering when the city’s improvement will be matched by an improvement in the conduct of its elected leaders.

“I have to tell you, everybody is waiting for what other shoes will drop,” said Jim Dinegar, president and chief executive of the Greater Washington Board of Trade. “Or is this the last one?”

It’s a sudden uncertainty. Two years ago, when Brown was an at-large council member, his path to the top was clear: With Gray (D) running for mayor, Brown was an overwhelming favorite to succeed him as council chairman. Brown, 41, would then become heir apparent to the mayor’s office, and with Gray in his late 60s, he might not have had to wait long.

Meanwhile, Thomas was headed to a landslide win of his own and would follow in Brown’s footsteps as chairman of the powerful Economic Development Committee — and perhaps as council chairman when Brown sought the mayor’s office.

But what some saw as a smooth transition from an old generation of city leaders to their children’s generation got complicated.

Thomas won his race, but his nonprofit fundraising came under scrutiny, leading to a city investigation that uncovered his embezzlement. Brown also sailed to a 2010 victory, but not before primary opponent Vincent B. Orange raised cutting questions about Brown’s 2008 campaign fundraising and Brown’s personal debt made campaign headlines.

Many assumed that the campaign issues — including more than $225,000 in unaccounted-for campaign funds — would lead to Brown’s demise. The debt proved to be more fateful.

With Brown out and Gray politically wounded, the leadership vacuum in city politics is likely to continue for months.

Next week, the council’s 12 remaining members will meet to pick an acting chairman from one of the four members elected citywide. It will be the third time an interim chairman has been chosen in the council’s short history. The other occasions came after tragedies of a different sort: John A. Wilson’s 1993 suicide and David A. Clarke’s 1997 death from brain cancer.

“We need to lower the temperature. We need to lower the sense of anxiety,” said council member Mary M. Cheh (D-Ward 3). “It’s better that it’s now happened so we can now accommodate ourselves to it. We need a period of quiet, we need a period of respite and we need a period of consolidation.”

Several members said privately that they intend to support 14-year veteran Phil Mendelson (D) to take over the chairman’s post until a special election can be scheduled — likely to coincide with the Nov. 6 general election.

If quiet is what the council wants, Mendelson fits the bill — a meticulous former council aide who in 2006 put “Nitpicker” on his campaign literature as a badge of pride. Where Brown’s penchant for luxury cars got his chairmanship off to a rocky start, Mendelson only recently and reluctantly replaced his decade-old Mercury sedan with a Ford hatchback.

Orange, who filled Brown’s old at-large seat in 2011, is also making an aggressive bid to fill the interim post. Orange, who narrowly won a primary this year to keep his seat, has pledged to colleagues that he will not seek the chairmanship in a special election.

While some Republicans on Capitol Hill see the charge against Brown as just the latest in a line of scandals that hurt the District’s case for self-governance, it’s not clear whether the controversies will have any substantive impact on congressional oversight.

Rep. Trey Gowdy (R-S.C.), the chairman of the subcommittee that handles District affairs, said his “approach to D.C. oversight has not changed at all,” noting the city’s strong finances.

But House Oversight and Government Reform Committee Chairman Darrell Issa (R-Calif.), who has pushed to give the District more budget autonomy and developed a good working relationship with Gray and other city leaders, took a dim view of Wednesday’s news.

His spokesman, Frederick Hill, said the case against Brown has “the potential to complicate some efforts.”

“These are serious accusations,” Hill said. “Resolving the situation quickly is critical to minimizing any damage to joint initiatives.”

Staff writer Mihir Zaveri contributed to this report.