"What If...?" is a term originally used by Marvel to split off their own series and answer the age-old question, making new stories that spurred from two simple words. Since then, it has come to be an easier way to say, "it doesn't feel like part of the main series."
That isn't to say the games that feel more like a What If are bad. Oftentimes, the opposite is true. What if this happened, or what if the franchise explored that missed opportunity further, or even what if someone else got the reigns are all questions that these sorts of games answer.
10 What If The Assassins Started In Ancient Egypt? (Assassin's Creed: Origins)
Assassin's Creed Origins goes back to the beginning of the whole Assassins vs. Templars debacle and shows how the factions were formed. The player was critical in starting the beginning of it all, from a time well before any of the the other games had even come close to appearing in.
Instead of focusing on historical events that are easy to look up, the developers got to be more creative in picking themes from ancient history instead. It was also the first game that had a real open world and more of an RPG element to it, which kickstarted the subsequent two entries into existence.
9 What If The Darkness Had A Name? (Don't Starve Together)
Don't Starve Together started out mainly as a multiplayer standalone counterpart to Don't Starve. However, due to the increasing popularity, love Klei puts into it, and the growing story, it slowly begins to feel more and more like a What If addition than anything else.
Maxwell is no longer sitting on the throne, and instead, it is Charlie who is the darkness. Canonically all of the characters available in Don't Starve Together all exist at the same time, each one trying to survive the constant for their own reasons.
8 What If We Started As Royalty? (Fable 3)
The previous two Fable games had the player start out in squalor and work their way up to grand heroism. They both end when they finally reach the epitome of their fame and presumably retire from their grandiose lives.
Fable 3 starts with the protagonist already at a royal level and falling from that, reclaiming their title halfway through, and then making decisions that affect the world around them.
7 What If The World Wasn't So Dark? (Final Fantasy IX)
The entire Final Fantasy franchise has an issue where it is overwhelmingly dark and gritty. Final Fantasy IX however is much less so. It's brighter, cuter in style, and tackles issues in a more light-hearted manner.
That's not to say that there isn't a lot of heaviness or difficulty by any means. It just felt like it was geared more towards a younger crowd and really played up to that during the story.
6 What If Roxas Got To Be The Star? (Kingdom Hearts: 358/2 Days)
Roxas has been a fan favorite within the Kingdom Hearts franchise since the second he appeared on screen. His whole story is a complicated mess, but fans love this dual-wielding Keyblade sweetheart.
385/2 Days allowed the player to be Roxas and go through his trials surrounding the Organization with him, build up lasting friendships with other characters similar to him, and finally give fans some real understanding as to what happened to him while being stuck playing Sora.
5 What If Link Went Somewhere Else? (Legend Of Zelda: Majora's Mask)
Majora's Mask is a direct sequel to Ocarina of Time, and considering how that one ended it's a confusing installment in its own right. Not even touching the complex ending of its predecessor, Majora's Mask has an assumed triumphant Link exploring a country outside of Hyrule.
While masks appeared in Ocarina of Time as a fun little side plot, they became a big deal in Majora's Mask. It was almost like someone said "What if one of these were a bad thing" and built a whole game around it.
4 What If There's Something Beyond The Universe? (Pokémon Ultra Sun & Ultra Moon)
The world of Pokémon is vast and full of strange creatures that can all do amazing things. Sun and Moon were the first to really explore the concept of things beyond the player's understanding, linking the worlds together with the concept of alternate timelines, universes, and spaces.
Ultra Wormholes were released as a vague explanation of what happened to those worlds and released a whole slew of Ultra Beasts which are Pokémon that either inhabited those alternate areas or were byproducts of them. Not to mention the fact it was the first in the main series to not have Gyms or a League, making it always a little like a spinoff or a What If instead of a regular game.
3 What If There Was Someone Before GLaDOS? (Portal 2)
The finale of Portal had it feel like Chell managed to escape the Aperture Science facilities, but was eventually patched and made it seem like she was recaptured or that was just another test in the simulation.
Portal 2 came along and had Wheatly take over as the big bad, condemning the outrageously powerful GLaDOS to a literal potato. Throughout the story, Chell learns some troubling facts about Aperture Science, including some startling hints at her own progenitors. It really humanized GLaDOS in a way that fans were not expecting, feeling a bit like a What If story in reverse, finding out who she might have been before being a computer.
2 What If The Hero Is Gone? (Suikoden 3)
So many games go about looking for a hero or forcing the heroism on one character in particular. Suikoden almost always has that be the Tenkai star. However, in the third installment, that title ends up falling to Thomas, who isn't even one of the three potential player characters.
The primary hero that everyone has been looking for and hoping for has been dead for ages, and it's up to one of the three other stars to try and take his place. Long-standing characters are either missing or on the opposite team, which sends some fans wondering if this was the first game where the player is not meant to be the hero in the first place, or what happens if a Tenkai doesn't step up to the plate.
1 What If The Game Takes Place Later? (Thief)
The 2014 reboot of Thief saw a modernized Garrett and a new town placed much further into the future. Reboots are perfect places for What Ifs, as the developers can take on a lot of questions and shape things into a new breath.
Many older fans were upset at this approach, but it really breathed in a lot of new life for a series that had been heavily hidden in much larger shadows of its genre.