You might be confusing Zebes and SR388. I believe SR388 is the home planet of the Metroids (as well as X), the planet you are on in Metroid 2. In Fusion, Samus is escorting those Biogenics personnel on the surface of SR388. There they discover the X parasite. It infects Samus there. They take samples of it aboard their research station and in the meantime the parasite multiplies in her body and she has a near fatal accident. A cure is discovered for the parasite using Metroid cells, the natural enemy of the X. However, as a result of the infection, the organic parts of her power suit have fused with her body (however that works). Meanwhile, the outer shell or the parts that were removed are possessed and controlled by X, creating SA-X, who is tearing through the space station.
The Metroid Prime manual even hints that it takes place before or at least very near Super Metroid. It talks about Samus seemingly destroying Mother Brain and the underground labs built on Zebes. Then the next paragraph talks about what happens next:
But the Space Pirates were far from finished. They immediately split their survivors into two main camps. One headed to Zebes to begin rebuilding their ravaged facility and resuscitating Mother Brain, Ridley, and Kraid. The second set out in search of a planet with powerful energy resources. They didn't search far before they discovered Tallon IV...
By the way, I am not a big fan of storytelling via a game's manual, but I'm pretty sure all this is alluded to in the game.
I know you could argue that perhaps she could have went on to SR388 for Metroid 2 (after destroying the labs on Zebes in 1), then she came back and destroyed the rebuilt labs on Zebes (and the planet itself judging from the explosion), then went on to Tallon IV to take care of the Space Pirates there, but... the older space pirate logs in Prime that you come across should reflect Samus' attacks on the rebuilt labs on Zebes, unless their was no communication between the Zebes labs and the Tallon IV labs.
Anyway, the morale of the story is don't read this much into a videogame series' storyline unless the story was pre-planned to be structured and arc like this from the beginning!