ACLU Sues in 46-Year Fight to Clear Sailor’s Name : Benefits: Son carries on battle for his late father who was denied veteran’s compensation after a WWII racial incident.

The American Civil Liberties Union of Southern California filed suit Tuesday in U.S. Claims Court to force the U.S. government to pay lost veteran’s benefits to the heirs of a sailor who was wrongfully given an undesirable discharge from the service during World War II.

The suit seeks to end the 46-year-old battle to clear Thomas Flanagan’s name and compensate Flanagan’s heirs for his wrongful discharge from the Navy, which accused him of being a ringleader of black sailors involved in a 1942 race riot in Vallejo, Calif.

“It’s a national injustice that has festered like an open wound for too long,” said Gary Williams, one of two attorneys handling the suit for the ACLU. “I’m happy that the case is about to be rectified, but I’m sad that Mr. Flanagan passed away before he could be vindicated.”

Flanagan, who died last year at 64, did manage to persuade the Navy in 1979 to change his discharge status to honorable, but until recently, that was his only redress. The Los Angeles resident had lost large amounts of money in back military pay and veteran’s benefits.

“He was bitter, very bitter,” Williams said. “In the end, he was angry that he did not get relief. He said, ‘I joined . . . to fight the enemy, but now I find the enemy was really within.’ ”

Last year, President Reagan signed special legislation sponsored by Rep. Mervyn M. Dymally (D-Compton) and Sen. Alan Cranston (D-Calif.) giving Flanagan’s heirs the right to bypass the statute of limitations and sue for his lost benefits. The ACLU’s suit was filed on behalf of Flanagan’s 16-year-old son, Thomas, who lives with relatives in Chicago.

Flanagan’s troubles began on Dec. 27, 1942, when he was a 19-year-old sailor at the Naval Ammunition Depot at Mare Island, Calif. While on liberty near Vallejo, he said he saw white Marines and shore patrolmen firing into an angry crowd of black sailors. He reported the incident to his commanding officer and asked what could be done about it.

A week later, Flanagan was accused of inciting the melee and put on a train out of town. His undesirable discharge was based on the accusation that he had “promoted ill feelings and racial prejudice and that he had been a ringleader in stirring up trouble and discontent among blacks,” according to court records.

In addition to costing him his veteran’s benefits, the taint of the undesirable discharge, Flanagan had said, made it difficult for him to return to his job as a steelworker.

As Flanagan told The Times in an interview three years ago, “I’m still not free. All these years of washing dishes--I could have been somebody.”

Williams said Flanagan’s case is symptomatic of a problem that existed for many black World War II and Korean veterans.

“Many blacks have been disciplined or discharged because of their race without any hope or sense of remedy,” he said. “It is not enough to change the discharge to honorable and say everything is OK. You have to do more to compensate those who have been seriously wronged by the system.”

Under the legislation approved by Congress, Flanagan’s heirs will be allowed to seek compensation only for loss of veteran’s benefits, not the loss of a career, Williams said.

The ACLU has asked experts to determine how much the lost benefits amount to in today’s dollars. Danna L. Cook, who is working on the case with Williams, said, “The government could settle out of court and end it very quickly, or it could take years if they decide to fight it.”

Williams said Thomas Flanagan “wants to see his father’s memory vindicated, and this is the way to do it.”

“It is one of the things his father talked about a lot, especially toward the end of his life,” he said.