The case was closed in November 2012, but reopened in January, when the alleged victim began cooperating.
In the midst of the investigation, President Barack Obama emphasized the importance of stamping out sexual assault during his May speech to this year's graduating class. Susan Burke, the alleged victim's attorney, went public days later, disclosing the investigation and what her client knew.
Burke, an outspoken lawyer who has represented more than 200 sexual assault victims, has said the academy tried to sweep the case under the rug to protect its reputation. The academy and an NCIS agent have said an investigation was vigorously pursued.
"Miller's decisions were informed by the findings and recommendations made by the Article 32 Investigating Officer, as well as by independent legal advice from the Navy's Region Legal Service Office and the Naval Academy's Staff Judge Advocate," the academy said in a statement.