The Side Stories are an alternative game mode in Pikmin 3 Deluxe, featuring two campaigns starring Olimar and Louie. The stories are arranged in several day-based missions, with each mission tasking the player to beat a certain requirement within its timeframe, in remixed versions of Story Mode areas. These can range from collecting treasure, not unlike Mission Mode, to more unique goals, such as retrieving a missing ship part. Once a mission is completed, a results screen is shown, and Olimar writes a log entry for the day. The first story, Olimar's Assignment, features 4 missions, while the epilogue, Olimar's Comeback, has 10. These stories also co-star the President, who issues the missions, gives tips during loading screens, and comments on the player's score when a day is finished.
Although every day is a part of an overarching plot, they are not connected in terms of gameplay, meaning what the player does in one day will not affect any other day. Throughout both stories, Olimar and Louie will make comments during gameplay based on certain events, much like the game's Story Mode, and when the day is done, Olimar will write a report. The next day only becomes available when the previous day has been completed and a medal has been earned. Any completed mission can be replayed at any point, and since they all have some score qualifier of some sort, the player can try to get better medals, or simply improve their high score. Some stages may feature areas or Pikmin types that the player may not have seen in Story Mode yet. Although nothing special happens for new areas, if the player is presented with a new Pikmin type, a one-page dialog window will show up before the mission, giving them a quick rundown of that Pikmin type.
This mode shares some gameplay rules with Mission Mode. The player does not have a mini radar, and although they can open the KopPad, no app will be available other than the standard radar. Onions cannot be interacted with, and the player only has the Dodge Whistle as an upgrade. Losing all Pikmin or losing a leader results in the day being over, and if the player gets stuck (e.g. by losing all Pikmin needed to destroy a certain obstacle), they will have to restart the day manually. Unlike Mission Mode, the player can activate or deactivate co-op play at any point during the day, and there are no after hours.
Olimar's Assignment is the first Side Story, and revolves around Olimar and Louie repaying another debt by collecting fruits and nuggets. It takes place before and during the main story. All of the days in this Side Story revolve around Olimar and Louie exploring the same main four areas the Koppaites explore in Story Mode, but with some layouts changed. All days start with a video log by Olimar, where he explains what he is doing, and incidentally shows Louie getting himself into trouble. These videos are the same videos found via Secret Files in Pikmin 3, though some lines of dialog are different.
Olimar's Comeback is the second Side Story, and focuses on Olimar and Louie repairing the Hocotate ship by collecting ship parts. It takes place after the main story. Each day has a different goal, and although their ultimate mission is to bring back the Hocotate ship, some days are dedicated towards planning or solving other problems. Their first day involves them gathering a Pikmin army large enough to help them with the task, some days require them to clear out enemies in the way, and some others simply task them to make a profit by gathering fruits and nuggets, among other scenarios. Instead of starting with a video log, every day of this mode starts with a simple written log by Olimar.
This Side Story has 10 total missions, and is unlocked after the player completes Story Mode.
For mission types besides "Battle enemies!", if a certain condition is met, it can become impossible to finish the mission but still be able to keep playing the level. When this occurs, the game will pause and display a message notifying the player that the mission's objective can no longer be met and ask if the player wishes to keep playing anyway. Choosing "Yes" resumes gameplay as normal, while choosing "No" ends the mission as if the timer ran out. This option is likely included to avoid forcing the player to waste their time waiting for the timer to run out in the event of not being able to progress further in the mission, as there is no option to end the mission early in the pause menu.
There are a few different scenarios that can be encountered that render a mission unfinishable: