The pod belonged to a Kryptonian diplomat, who used it to visit Daxam. In 1979 as Daxam was ravaged by solar storms, the diplomate tried to use his pod to escape the planet, but was killed by a Daxamite palace guard, who placed Mon-El into the pod. The pod then flew Mon-El away.
Upon escaping Daxam, the pod became stuck in the Well of Stars for about 37 years. In May 2016, it finally made its way to Earth, crash-landing in the outskirts of National City. Kara Danvers and J'onn J'onzz discovered the pod, with an unconscious Mon-El inside. The pod was then presumably taken and stored by the D.E.O..