Comments by one of Mr. Mueller’s lead prosecutors, disclosed in a transcript of a closed-door hearing, suggest that the special counsel continues to pursue at least one theory: that starting while Russia was taking steps to bolster Mr. Trump’s candidacy, people in his orbit were discussing deals to end a dispute over Russia’s incursions into Ukraine and possibly give Moscow relief from economic sanctions imposed by the United States and its allies.

The theory was offered almost as an aside by the prosecutor, Andrew Weissmann, during a discussion of contacts between Mr. Trump’s former campaign chairman, Paul Manafort, and a longtime Russian associate, Konstantin V. Kilimnik, whom investigators have linked to Russian intelligence.

A closer look at the transcript, released late Thursday, shows that the prosecutors have been keenly focused on discussions the two men had about a plan to end the conflict that followed Russia’s invasion of Ukraine and annexation of Crimea in 2014.