Aftermath ends up being an interesting mirror and echo to the main MK11 story. Both feature heroes allied to someone they aren't sure they can trust to beat Kronika (Raiden in the main game, Shang here). Both see classic, uber powerful characters reunited with allies they have been long divided from (Liu Kang and Raiden, now Shao and Sindel) and then sees the resulting duos utterly stomp everything in their way. And both end with a Mortal Kombat champion gaining supreme power and trying to lay claim to the hourglass.
Also, as much as MK11's story was giving off last chapter vibes, with as many character relationships as it closed out and payed off (Cassie/Sonya, Scorp/Hanzo, Raiden/Liu, Sonya/Kano, Kotal/Shao, Kitana/Shao, Sub/Hanzo, Jax/his trauma etc) and a good ending that is almost the perfect happy ending for the heroic characters, Aftermath leans even harder into that vibe in one major way, bringing us around all the way full circle, back to the very beginning. Liu Kang vs Shang Tsung for the fate of the realms.
Essentially, Fujin let the bad guys win, because Liu Kang told him it was necessary. Which is almost an odd nod to MK9, when Liu Kang couldn't go along with Raiden's crazy plan to let Shao Khan win, even though doing so ultimately proved to be the correct play.
Also, as much as MK11's story was giving off last chapter vibes, with as many character relationships as it closed out and payed off (Cassie/Sonya, Scorp/Hanzo, Raiden/Liu, Sonya/Kano, Kotal/Shao, Kitana/Shao, Sub/Hanzo, Jax/his trauma etc) and a good ending that is almost the perfect happy ending for the heroic characters, Aftermath leans even harder into that vibe in one major way, bringing us around all the way full circle, back to the very beginning. Liu Kang vs Shang Tsung for the fate of the realms.
I think, given Fire God Liu Kang's response to Shang later in the Hourglass chamber, that we're supposed to believe that Fujin DID recognize Shang in his disguise, but was only pretending not to because he was in on FG Liu Kang's plan. Recall the opening scene of Aftermath, where Liu pulls Fujin aside and tells him something, which Fujin says won't be easy, and which Liu says to keep it secret from Nightwolf? Fujin KNOWS that Shang Tsung has to beat Kronika. FG Liu Kang has revealed that Fujin is going on a sacrifice play, to make sure that Shang Tsung gets the crown and gets to Kronika, no matter what other cost must be paid. Because Liu intends to take the crown back and simply rewrite over whatever goes wrong when he recreates time.Fujin not knowing Shang was disguised as his brother but Baraka knowing earlier in the game was very silly.
Essentially, Fujin let the bad guys win, because Liu Kang told him it was necessary. Which is almost an odd nod to MK9, when Liu Kang couldn't go along with Raiden's crazy plan to let Shao Khan win, even though doing so ultimately proved to be the correct play.