In terms of the series chronology, this game takes place between Metroid Prime: Federation Force and Super Metroid. Ridley's surprise appearance also confirms that the Prime games are canon; he's still recovering from the events from Corruption and has fewer cybernetics attached to him.
Connection to Other Media
Samus's death animation shows that she's wearing her Other M Zero Suit under her armor. The sound effect is taken directly from Super Metroid. In the original Metroid II, her character sprite merely dissolved.
Getting the good ending on Hard Mode results in Samus having green hair. This is an homage to the Justin Bailey code in the original Metroid. If you get the best ending on Hard Mode, she'll be wearing the full Justin Bailey suit instead of the Zero Suit. Getting the best ending on Fusion Mode results in her wearing the same outfit she used for the best ending in Metroid Fusion.
The box art is an homage to that of the original Metroid II. The special edition takes it a step further by having a reversible cover, with the older game's box art on the other side.
The last cutscene shows a Hornoad being infected by an X Parasite. This is a nod to Metroid Fusion, in which the X Parasites become a major threat due to the Metroids - their only natural predators - being wiped out by Samus. This is also foreshadowed via the Chozo Memories, which show the Chozo creating the Metroids to eliminate the parasites.
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