Allen & Co., the New York-based investment bank, is best known for its annual conference in Sun Valley, Idaho, where billionaires such as investor Warren Buffett and Microsoft’s William Gates III mingle with entertainment industry executives such as Oprah Winfrey, Harvey Weinstein, and Sumner Redstone and technology pioneers such as Apple’s Steve Jobs and Google’s Sergey Brin.

A longtime partner in the firm, Charles Robert Allen III, who is the son of its late founder, the “Shy Midas of Wall Street,” Charlie Allen Jr., regularly complained that the event was “excessive” and “so expensive to put on,” a friend of Charles Robert Allen’s, who requested anonymity, told The New York Sun.

Now Charles Robert Allen’s streak of contrarian independence is under the scrutiny of a Nassau County, Long Island state judge, Joel Asarch, in a sealed proceeding that centers on investments the former banker, now 77, made in rural radio stations.

A son of his, Luke Allen, is claiming “my father has been defrauded of some $88 million,” according to court documents obtained by the Sun. The court case began when Charles Robert Allen’s wife of more than 50 years, Grace Allen, sought to have her husband legally declared mentally incapacitated. Under a court order, Luke Allen is the guardian of his father’s assets.

For his own part, Charles Robert Allen is resisting his family’s efforts to prevent him from controlling his fast dwindling fortune. Around dawn on November 29 of last year, Charles Robert Allen sent a desperate fax to Judge Asarch.

“With all due respect to the court, I wish to end the guardianship,” Charles Robert Allen wrote. “If the purpose is to stop me from making bad investments it is un-American. Should a guardian have been appointed for my dad because he was at one point bankrupt?”

The case raises some issues similar to, but not exactly the same as, the Brooke Astor drama that captivated Manhattan society until the philanthropist died last year at age 105.

Allen & Co did not respond to several inquiries. The firm is headed by Herb Allen, a first cousin to Charles Robert Allen. Charles Robert Allen left Allen & Co as a partner when he was 65 in the mid 1990s. He sold his stake in the firm, telling the same friend that he received $365 million for it. The amount could not be confirmed. A second source close to the Allen family contested that figure, saying, “not only is that number implausibly high, but the idea that Bob Allen would have said how much money he received is contrary to everything I know about him.”

Although he no longer goes into the office, Charles Robert Allen never quite retired. From his Sands Point estate, he has devoted himself to his lifelong passions of investing and exercise. His estate has its own outdoor track, one-eighth of a mile long.

“I think he left Allen & Co with ambition,” another source close to the family said. “I think he wanted to prove that he could be as successful as those other guys at Allen & Co.”

Charles Robert Allen saw his big opportunity in the radio business, which he had long dabbled in with a small portion of his money. The investments, which increased in amounts in recent years, are the subject of an Allen family investigation into whether Charles Robert Allen’s partners defrauded him of his money.

In a court affidavit, Luke Allen alleges that the entrepreneurs who received the investments “re-directed these funds” to other entities in which Charles Robert Allen had no stake. A report commissioned by Luke Allen, and undertaken by the accounting and business consulting firm RSM McGladrey claims “that funds may not have been used as intended, raising the specter that potentially fraudulent activities may have occurred.”

The documents are under court seal in Nassau County. But they are publicly filed in court in Chicago, where subpoenas for relevant business records are being litigated.

In an interview, the businessman with whom Charles Robert Allen invested his money, Christopher Devine, denies any wrongdoing and says that the investments are only a short time away from seeing profitable returns.

Charles Robert Allen’s partnership with Mr. Devine goes back to the 1980s, when Mr. Allen was still at the family firm. Although Mr. Devine is a generation younger than Charles Robert Allen, the two bonded over their shared interest in running. Mr. Devine, who now owns the rights to several marathons, including those in Los Angeles and Las Vegas, had recently run across the country in 74 days.

Until Luke Allen put an end to the habit this year, Mr. Devine spoke with Charles Robert Allen every day for the last 21 years, with only three exceptions, Mr. Devine said.

With Charles Robert Allen’s backing, Mr. Devine has purchased rural radio stations and radio licenses across the country, with the hopes of moving them into larger markets.

Currently Charles Robert Allen, as well as other investors, have a stake in licenses for 30 radio stations and 16 stations that are up and running, Mr. Devine said. The most valuable of the existing stations are in Portland, Oregon, Las Vegas, and Salt Lake City, Mr. Devine said.

Charles Robert Allen’s investments went to a company in Chicago, Superior Broadcasting Company, in which he is the majority shareholder. Yet the radio licenses and stations aren’t in Superior’s name. They are “actually owned by an obscure web of companies,” Luke Allen claimed in a court affidavit. About $30 million of Charles Robert Allen’s money went to a company called Lakeshore Media, which the Allen family has no stake in, Luke Allen claimed.

It’s possible that is how Charles Robert Allen wanted it done. Mr. Devine said that Charles Robert Allen preferred the expenditures to be made by companies in which he had little connections.

“He didn’t want any of the potential liabilities connected with being an officer or a shareholder,” Mr. Devine said.

In a letter to his attorneys in 2006, Charles Robert Allen notes that “my business practices with Devine are unconventional” and that “for several years many of the corporate formalities have not been observed.”

In the 15 years before 2001, Charles Robert Allen had invested about $12.5 million over with Mr. Devine, according to court records. In recent years, he began committing a far larger share of his fortune, investing $75 million more with Mr. Devine between 2002 and 2006, according to court documents.

Charles Robert Allen’s net worth is unknown, and estimates range widely. Luke Allen, whose affidavits do not mention how much Charles Robert Allen received for his share of Allen & Co., claims that his father’s investments with Mr. Devine exhausted “nearly all his liquid assets.”

To come up with the funds, Charles Robert Allen borrowed $35 million from J.P. Morgan Chase against his investment grade bond portfolio, according to one of the son’s affidavits.

In an interview, Mr. Devine described Charles Robert Allen “as brilliant, and sharp as a tack.” He described the guardianship proceeding as a “shame” and suggested that Luke Allen’s motivation was simple: to undo investments he disagreed with.

“Luke just wants it back, and he wants it back now,” Mr. Devine said.

He said that over the years Charles Robert Allen has recouped $30 million on his investments with him so far.

“Every dime is accounted for,” Mr. Devine said. “It’s an invested $80 million that hasn’t harvested yet.”

Luke Allen, through his lawyer Kent Yalowitz of Arnold & Porter LLP, declined to comment for this article. Luke Allen, one of three surviving sons adopted by the Allens, lives off a gravel road in rural Pennsylvania where he raises horses.

Friends and acquaintances say they have received harrowing phone calls from Charles Robert Allen in recent months.

“The last couple of times, he sounded quite desperate,” an investor in Lakeshore Media, Neal Robinson of Williamsburg, Virginia, said, describing his conversations with Charles Robert Allen. “He pleaded with me like a prisoner to please help him, to please meet with his son and his representatives.”

Charles Robert Allen’s mental capacity is disputed. Mr. Yalowitz, Luke Allen’s lawyer, described Charles Robert Allen as “a man of diminished capacity,” in a Chicago courtroom last year, according to a transcript.

A related lawsuit filed by a neighbor of Charles Robert Allen, Richard Davis, a backgammon partner and investor in Superior, claims that Mr. Davis purchased “large quantities” of mouth wash and hundreds of pairs of matching bedroom slippers for Charles Robert Allen at Mr. Allen’s request.

Contacted by telephone at his home on Long Island, Charles Robert Allen declined to comment.