Battlestations: Pacific expands on Battlestations: Midway in several ways, adding new combat features such as more advanced submarine combat, more easily customizable planes and ordinance loads, island invasions, which have effects on the battle at hand. New weapons, planes, and ships were added, such as HVAR Rockets and experimental fighters, including the Kikka and Shinden, along with kamikaze units, such as the Ohka and Kaiten; there are also some more conventional aircraft and ship additions.
The most drastic addition is that of the Japanese campaign, which tells a "what if" story in which Japan is victorious at the Battle of Midway and continues their war effort beyond that point to invade Hawaii, trade technology with Germany, and defeat the United States of America, with an ending cinematic of General Douglas MacArthur signing a peace treaty on the IJN Yamato in San Fransisco Bay, meant to echo the surrender of Japan on the deck of the USS Missouri.
It is also possible to, at the start of the attack on Pearl Harbor, "kill" the two main characters of Battlestations: Midway. If the player managed to sink Henry's PT boat, the pilot would comment "His name was Henry. This is not his story." After shooting down Donald's more advanced plane, he would go on to comment that "Fighter ace, huh? At least you died in the air." pointing back to Donald's death on the USS Yorktown at Coral Sea.