Heartwarming / Metroid Fusion

• Samus mentally refers to the computer ordering her around as Adam, unaware that it actually is him. For most of the game, it is simply a way for her to receive orders and upgrades from the Federation. Adam remains strictly loyal to the Federation's mission parameters until Samus accidentally calls him by name - a short while after this moment, the real Adam shines through and helps Samus come up with a plan to take out the X for good.
• 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.
• 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.
  • As of the Retcon in Metroid: Samus Returns it's now three times, thanks to saving Samus from Ridley while they were making their departure.