After defeating all other Metroids, the lava will recede completely, revealing the path to the Metroid Queen's lair. This is the final confrontation, and you must be at your absolute best. Ensure you have full energy and missiles before entering.
The path to the Queen is usually straightforward once all other Metroids are eliminated. There might be a final save point just before the entrance, so use it. This is it, Samus. The fate of the galaxy rests on your shoulders.