Misiewicz would refer to Francis as "Big Brother" or "Big Bro" in emails from a personal account, while Francis would call him "Little Brother" or "Little Bro," according to the complaint.
The company bilked the Navy out of $10 million in just one year in Thailand alone, U.S. Attorney Laura Duffy said.
In December 2011, the two exchanged emails about the schedule of the USS Blue Ridge, investigators say. According to court documents, Francis wrote Misiewicz: "Bro, Slide a Bali visit in after Jakarta, and Dili Timor after Bali."
The complaint alleges Misiewicz followed through on the demands: In October 2012, the USS George Washington was scheduled to visit Singapore and instead was redirected by the Navy to Port Klang, Malaysia, one of Francis' preferred ports where his company submitted fake contractor bids.
After Francis offered Misiewicz five tickets to a Lady Gaga concert in Thailand in 2012, Francis wrote: "Don't chicken out bro we need u with us on the front lines," according to court documents.
The federal government has suspended its contracts with Francis.
The defendants face up to five years in prison if convicted of conspiracy to commit bribery.