Some future Metroid game manual wrote: After their infrastructure was devastated by Samus' mission on Zebes, the space pirates began pursuing another project hoping to lead them to supremacy, with the reconstruction of Zebes and breeding of metroids taking a back seat to this new plan. After this new threat was defeated by agents of the Federation (including Samus), the space pirates returned to their previous plan of using metroids to conquer the Federation. Concerned that the space pirates might return to the metroids' homeworld and acquire them without the Federation knowing, the Federation military sent multiple forces, culminating with Samus, to eliminate the threat of this happening by exterminating the metroids on SR388.
So, none of the details that would identify this "new project" as Phazon, nor any of the details of the events that took place other than that Samus was involved in it, only the mention that "something else happened". For those of us who have played the Prime series, we either know what it was, or alternatively can choose to ignore it and imagine something of our own in its place.