In February of 1944, Assistant Attorney General Tom Clark sought U.S. Attorney General Francis Biddle 's permission to charge the Shitara sisters with the capital offense of treason. Noting the large number of escapes from POW camps, Clark argued that prosecuting the Shitara sisters would have the valuable effect of deterring other people from rendering assistance to escaped POWs. On May 2, 1944, a federal grand jury in Denver indicted the three Shitara sisters for treason and for conspiracy to commit treason, specifying the provision of maps, the provision of clothing, and the drive into New Mexico as the "overt acts" of which Article III of the U.S. Constitution requires proof by two witnesses.

Trial commenced on August 7, 1944, in the courtroom of J. Foster Symes, Colorado's lone federal district judge. The prosecutor's task was to prove not only that each of the sisters was responsible for one or more of the "overt acts" of treason, but also that in committing those acts each woman acted with treasonous intent, an intent to "give aid and comfort" to an enemy of the United States. This meant that the prosecutor had to show that the women intended not just to help Haider and Loescher personally but to injure the United States out of allegiance to an enemy.

The prosecution had little difficulty proving through the testimony of two witnesses that the sisters committed the overt acts. That testimony came, ironically, from Haider and Loescher, the enemy soldiers to whom they were accused of giving aid and comfort.

The difficult thing to prove was the sisters' criminal intent. What made this difficult was that Haider and Loescher told a variety of shifting stories in the months after their arrest. Upon arrest they did not mention the sisters at all. Then they told investigators that the women had tried to dissuade them from escaping when the subject first came up at the onion farm. Then they told investigators that they had had sex with two of the women but asked that this not be publicly disclosed. Then, when asked if the episode was just a "romantic escapade," one of them maintained that he believed the women had done what they did "to help Germany," and that he knew they "feel allegiance to Japan and to its ally Germany" because they were "definitely Japanese and probably ha[d] not been accepted by Americans." Then one of them sent a pre-trial letter to Judge Symes reiterating that the men had had to "take many troubles by words and by letters" to persuade the reluctant women to help them and insisting that they, and not "the seduced women," were the guilty parties.

When Haider and Loescher took the witness stand at trial, their stories changed yet again, and in ways that were unhelpful to the prosecution on the question of the sisters' intent. Haider asserted that he was an "anti-Nazi" who wanted to escape from Camp Trinidad so that he could join a resistance movement to "fight against the Hitler gang." Loescher, for his part, said that he had been severely wounded in combat and knew he could never fight again; he did not want to return to combat but simply wanted his freedom. Neither said a word suggesting that the women were acting out of disloyalty to the United States or allegiance to Germany or Japan.

The sisters did not testify in their own defense, and therefore did not supply any evidence about what their intent was in helping the POWs. On the issue of criminal intent, the jury knew only that the women had acted to help the POWs in their escape, that they were cheating on their husbands, and that they were ethnically Japanese.

In his summation to the jury, the lawyer for the sisters argued that the case was about love, not treason. He alluded to the intimacies between the men and the women and argued that the case was about the "frailty" of women in love. He noted that the women were married, and acknowledged that they had done wrong, but maintained, in effect, that betraying their husbands was not the same as betraying their country.

The federal prosecutor responded in kind. Calling the sisters "little Benedict Arnolds in skirts," he reminded the jury that "these were married women" who "were not true to their husbands" or "to the United States of America."