- How Adam started the ship up in the ending. After Samus rescues the Dachoras and Etecoons for the second time, once prior during Super Metroid, they help rescue Samus and Adam at the end of Fusion. Afterwards, Samus reflects on her actions with her computer C.O., who we now know is Adam. But when Adam is asked about how he started the ship manually, there's a group shot of the Drachoras and Etecoons taking a well-deserved nap in the corner afterwards. So cute, it Tastes Like Diabetes.
- The Metroid vaccine that saves Samus from her X-Parasite infection at the beginning of the game came from the baby Metroid from Super Metroid. You know, the one that sacrificed itself to save its mother from Mother Brain? This means the Baby saved her twice over—once while she was fighting Mother Brain, and once from beyond the grave from the natural prey of the Metroids.
Heartwarming / Metroid Fusion