Nuradin Abdi completed his prison sentence in August and was in federal custody in Louisiana while final preparations were made to return him to Somalia.
Immigration and Customs Enforcement on Monday confirmed the deportation.
Abdi’s sister, Kaltun Karani, says the family is happy that Abdi is a free man.
The Justice Department accused Abdi of suggesting a plan to shoot up an unidentified Columbus shopping mall during an August 2002 meeting at a coffee shop with two friends, both of whom were later convicted of terrorism charges.
Early reports indicated the threat might also have included bombing a mall.