He told IGN that 'The Day We Died' will link back to the season's early episodes, which saw Olivia (Anna Torv) replaced by her doppelganger Fauxlivia.
"Very much, the season was designed as a chapter and it will play out that way," he claimed. "And the very end of the season hopefully will make you sort of revisit and look at everything that's happened all year through a fresh pair of glasses."
Pinkner also revealed that the script for the finale had not been altered following the news of the show's renewal.
"Not a word [has changed]," he insisted. "But to be fair, we wrote the episode, perhaps foolishly, assuming that we would be on for season four. We never for one second entertained that [the season finale] would be the end of the series."
The showrunner added that he would "certainly hope" to be given notice when the time does come for Fringe to end.
"The studio and the network know that we have an ending [in mind] and that for a long time we have been building towards [that] ending," he said. "So we anticipate getting to tell the story in the way and the manner that we want to."
Fringe returns to Fox on April 15. The season finale will air on May 6.
> The past and future of Fringe