Alright, I've been giving this some thoughts. No, this isn't about the "genocide of one species on planet SR388 leads to an upset of the entire ecosphere" topic. This is about that infamous of lines, probably the most well-known phrase of the entire series:
The last Metroid is in captivity. The galaxy is at peace.
Metroid: Samus Returns is a very important entry in the franchise, because it's a remastered retelling of the most important part of the entire series: the genocide of the Metroids from their home planet. All the other games of the franchise lead up to or stem off of this chapter of the story. Samus kills the Queen Metroid, and then finds a Metroid egg, which hatches before her eyes and imprints on her like a child to its mother. (Or, her mother, as Other M alludes.) Samus then takes the Baby off the planet and to scientists, who study the Metroid and find that its capabilities could help the universe, instead of being used as weapons like the Space Pirates intended. In busts Ridley, who takes the Baby back to Zebes, where a rebuilt Mother Brain uses the new Tourian facility to clone Metroids from the Baby, using beta radiation. Samus infiltrates Zebes again, kills some of those clones, and then ends up killing Mother Brain, but not before the climax of the series: The Baby gives her life for Samus, and the Last Metroid explodes, never to skree again.
...But... IS she the last Metroid?
Let's back up a little.
Federation surveyors find a Metroid on planet SR388. Space Pirates grab the Metroid before it could be delivered to Federation HQ for studying. Pirates take the Metroid to their base on Zebes, where Mother Brain begins cloning the Metroid for Pirate usage.
Pirates take some Metroid specimens in their research frigates. When Samus arrives for her Zero Mission, the Pirates were elsewhere. Or fighting the Federation fleet, blockading them. Samus destroys some Metroids, and then destroys Mother Brain. According to a lore entry in Prime, three research vessels were in Zebesian orbit when Tourian blew up. This doesn't count the Mothership landed on the surface.
One of those vessels was the Orpheon, which Samus later finds over Tallon IV. The Orpheon transported Metroids off of Zebes, to the Pirate encampment on Tallon IV. These Metroids are experimented on with Phazon, and somehow they lose their imperviousness to anything but the Ice Beam, becoming weaker but still deadly.
Later still, Samus finds Tallon Metroids on Aether, as a result of a Pirate vessel crash-landing there after being pursued by Federation Marines. Some of the Ing possess some of the Metroids, but the Pirates maintain a lab where Metroid specimens are kept (largely) in check. At a certain part of the adventure, Samus finds the Metroids have begun breeding.
After Dark Aether's destruction, Pirate forces manage to escape the planet before the Federation comes in and claims whatever Phazon was left behind. Dark Samus snuck aboard their vessel and corrupted them. It can be assumed that they also had some Tallon Metroid specimens with them, and those too were corrupted. We can find Phazon Metroids in Skytown on Elysia, which were escaped specimens from a xeno research lab which might've either been Pirate based, or Chozo based. We also later find Phazon Metroids on the Pirate Homeworld, and then again on the source of all Phazon, Phaaze.
Then Samus destroys Phaaze, supposedly rendering all Phazon in the galaxy inert. This means that Pirate vessels charged by Phazon were stranded; cybernetic and genetic enhancements were shut down (yikes!), and Phazon-infused creatures self-destructed. I suppose this means all Phazon Metroids were simultaneously wiped out.
After these occurrences, another Metroid was sighted in the Bermuda system by the Federation Force.
AND THEN, according to the usual interpretation of the Metroid timeline, the Federation council unanimously agreed, that Metroids had to be exterminated. Cue Metroid II / Metroid: Samus Returns.
Hopefully, you can see where I'm going with this.
The Federation Council gives Samus the task with destroying all remaining Metroids, which happen to reside on the planet of their initial discovery: SR388. But... can it honestly be said or confirmed that those were indeed the last Metroids?
As you can see, there's a lot that needs to be answered, before we can safely say that yes, SR388 is the last vestige of Metroids in the galaxy. And before we can say that the Baby Metroid is indeed the last Metroid.