"Walternate" is the nickname given by Walter Bishop to the Alternate Universe version of himself. Walter gave him the nickname while observing him through the dimensional window. He is the true father of Peter Bishop. In 1985, Walternate, like our Walter, was working on a cure for the disease that was killing Peter. While he was working on the cure he was distracted during a test by the Observer and didn't notice that his latest concoction was almost successful, causing him to abandon that combination entirely.

Our Walter was watching this through the window, and realized that he could cure the other Peter, leading him to create the doorway to the other world. However, since Walter's supply of the cure was destroyed, the only way he could save the other Peter was by taking him back to our side. Although he originally intended to return the boy to his real home, he couldn't bring himself to do it after his wife Elizabeth Bishop discovered him, and saw how he looked exactly like her dead son.

It was revealed at the end of Northwest Passage that the "Mr. Secretary" whom Newton brought over from the other universe was, in fact, "Walternate".

In Over There: Part 1, it is revealed that Walternate is the secretary of defense. He is much colder and more ruthless than his counterpart, presumably both from never having been committed as well as the loss of his son. It is Walternate who is the mastermind behind the Pattern, and his ultimate goal is to destroy our universe, believing that doing so will repair all the damage caused to his. When faced with an "invasion" from our universe, he enacts a plan to overwrite our Olivia's memories and make her believe she is her counterpart, for an unknown purpose, as well as sending the Alternate Olivia into our universe to pose as her double.

Like our Walter Bishop, Walternate is portrayed by John Noble.