On the outbreak of the Spanish Civil War he wanted to immediately join the Abraham Lincoln Battalion, a unit that volunteered to fight for the Popular Front government against the military uprising in Spain. The American Communist Party rejected the idea claiming he was more important to the cause in America.
Thompson was an excellent soldier and he commanded the Mackenzie-Papineau Battalion at Fuentes de Ebro. As Cecil D. Eby, the author of Comrades and Commissars: The Lincoln Battalion in the Spanish Civil War (2007), pointed out: "Never popular among the men, Captain Robert Thompson did attract admiring glances that morning as he stood exposed on the parapet of a trench directing his men into their positions."
On 25th September 1938, Juan Negrin, head of the Republican government, announced for diplomatic reasons that the International Brigades would be unilaterally withdrawn from Spain. However, General Francisco Franco failed to reciprocate and German and Italian forces remained to continue the struggle.
During the Second World War Thompson, like many members of the Abraham Lincoln Battalion, joined the US Army. As Hank Rubin pointed out in Spain's Cause Was Mine (1997): "We were pariahs to our government. When Brigaders volunteered for the armed forces in World War II, the official army line, at first, was that we were not to be sent outside of the continental limits, so that we would not have contact with European communists. This ruling was later successfully challenged. Even so, most of us were sent to the Pacific combat zone."
Thompson served as a non-commissioned officer in the 32nd Division in the Pacific. He was cited for "extraordinary heroism" during the New Guinea Campaign and won the United States Army's Distinguished Service Cross.
On 20th July, 1948, twelve party leaders, included Thompson, John Gates, Eugene Dennis, William Z. Foster, Gus Hall, Benjamin Davis, Henry M. Winston, and Gil Green, were arrested and charged under the Alien Registration Act. This law, passed by Congress in 1940, made it illegal for anyone in the United States "to advocate, abet, or teach the desirability of overthrowing the government".
The case began in March, 1948. The men were defended by George W. Crockett. It was difficult for the prosecution to prove that the twelve men had broken the Alien Registration Act, as none of the defendants had ever openly called for violence or had been involved in accumulating weapons for a proposed revolution. The prosecution therefore relied on passages from the work of Karl Marx and other revolution figures from the past.
The prosecution also used the testimony of former members of the American Communist Party to help show that they had privately advocated the overthrow of the government. The most important witness against the leaders of the party was Louis Budenz, the former managing editor of the party's newspaper, The Daily Worker.
Another strategy of the prosecution was to ask the defendants questions about other party members. Unwilling to provide information on fellow comrades, they were put in prison and charged with contempt of court. The trial dragged on for eleven months and eventually, the judge, Harold Medina, who made no attempt to disguise his own feelings about the defendants, sent the party's lawyers to prison for contempt of court. After a nine month trial Thompson and other leaders of the American Communist Party were found guilty of violating the Alien Registration Act and sentenced to five years imprisonment.
Thompson jumped bail but was arrested in the California Sierras in 1954. He was given an extra four years in addition to his original three. John Gates pointed out: "In a few instances... men hoped to curry favor with the authorities by physically attacking Communist prisoners. This occurred to Bob Thompson who was hit over the head from behind with a lead pipe by a fascist Yugoslav prisoner fearing deportation to Yugoslavia and figuring that this way he could get out of it."
In April 1956 Eugene Dennis, published a report on the American Communist Party. As John Gates pointed out that it "was a devastating critique of the party's policies over a whole decade. Like all reports, it was not only his own, but had been discussed and approved by the National Committee members in advance. Dennis characterized the party's policies as super-leftist and sectarian, narrow-minded and inflexible, dogmatic and unrealistic." Thompson, William Z. Foster and Benjamin Davis, constituted a minority of the leadership that led the attack on Dennis.
Robert George Thompson suffered a fatal heart attack on 16th October, 1966. The United States Army posthumously denied him a burial at Arlington National Cemetery. However, this decision was reversed after a campaign by his widow. As the journalist, Murray Kempton wrote: "And so, an American who was brave has been judged and disposed of by Americans who are cowards of the least excusable sort, cowards who have very little to fear. Yesterday the Army called Robert Thompson's widow and said that it would send his ashes wherever she wished. Wherever those ashes go, the glory of America goes with them."