Lt.-Gen. Steven Whelan wiped away tears this morning as military prosecutors asked the judge in his court martial to withdraw the case against him.
Whelan had pleaded not guilty to one count of conduct to the prejudice of good order and discipline for changing a performance report in 2011.
The military alleged he gave the complainant in the case, a woman who was under his command at the time, a better score to prevent her from telling senior commanders about flirtatious emails Whelan had sent her before they worked together.
Prosecutors dropped a different charge at the beginning of the court martial last week related to what the military called an inappropriate relationship with a subordinate.
This morning, prosecutors asked the military judge, Cmdr. Martin Pelletier, to withdraw the remaining charge, based on "an assessment of the evidence."
Pelletier ruled on Friday that the emails at the centre of the case could not be admitted as evidence for the prosecution.
Prosecutors declined an interview request this morning.