If you look at the overall timeline, It likely takes after Metroid Prime: Federation Force where a special ending shows Sylux hacking a stasis tube that causes the Metroid Egg to hatch. Federation Force came after Metroid Prime 3: Corruption (Where Sylux is seen following Samus). This puts it before Metroid Samus Returns where the Metroids are being exterminated minus the Baby Metroid. That being said, it takes place before long Metroid Dread.

https://metroid.fandom.com/wiki/Metroid_timeline?so=search

Metroid timelineWikitroid