[1] On July 24, the Mets traded Whalen and John Gant to the Atlanta Braves for Juan Uribe and Kelly Johnson.

[10] On November 28, 2016, Whalen and Max Povse were traded to the Seattle Mariners organization in exchange for Alex Jackson and Tyler Pike.

Whalen announced his retirement from professional baseball on February 25, 2019, citing his battle with depression and anxiety as the main reason for doing so.

[13][14] On January 27, 2020, Whalen came out of retirement and signed a minor league contract with the New York Mets organization.

[17] On March 5, 2021, Whalen signed with the West Virginia Power of the Atlantic League of Professional Baseball.

However, on May 5, before the ALPB season began, Whalen signed a minor league contract with the Minnesota Twins organization.

[18] In 11 appearances split between the Double-A Wichita Wind Surge and the Triple-A St. Paul Saints, Whalen struggled to an 0-4 record with an 8.63 ERA and 19 strikeouts.

[25] Despite being an effective ground ball pitcher, Whalen stated that he would actively seek the strikeout whenever a two-strike count arose.