References to the Secret Wars appeared long after the self-titled stories were all wrapped up. Thor 383 has an untold story from SWI and Quasar 8 references Iron Man's new armor. What If 114 explored the happenings if the heroes stayed on Battleworld and a TPB was published for SWI's 20th anniversary.

Fantastic Four revisited the Beyonder and explored his origins in 1988. References to the Beyonder were made in Fantastic Four 317 and 318 while a new battle dubbed Secret Wars 3 was fought in issue 319. Deadpool Team-Up featuring Widdle Wade popped up in late 1998 poking some fun at the whole Secret Wars in general.