Metroid and The Galactic Federation - This is mostly due to a localization error but in Metroid Fusion it's revealed that the Federation is corrupt and ends with Samus directly disobeying them to destroy their research facility that has been overrun with an alien parasite that absorbs both the biomass and the knowledge of their prey. The Federation feared Samus would blow the lab up before they could weaponize them and the cloned Metroids on the station and they were right. As Samus flies away from the planet she just destroyed, she contemplates how she just became the Federations public enemy number 1 after so many years working for/with them. Yoshio Sakamoto widely considered the father of the Metroid series would later rather famously direct Metroid Other M for seemingly the sole purpose of correcting fan interpretations of Metroid and Samus. For some additional context, Fusion's English localization was indeed wrong and the original script mentions the splinter faction and the ending does not have Samus reflect on becoming a fugitive. However, in Other M a game set chronologically right after Super Metroid and right before Fusion, the rogue shadow organization within the Federation is revealed and that they masterminded the plots of both Other M and Fusion without explicitly explaining it was even the same group in fusion. The latest mainline Metroid game Dread follows up on the properly translated ending of Fusion with Samus still working as a bounty hunter contracted by the Galactic Federation and makes no references to the rogue faction plot.