Samus lays the eggs.

"Now thisss isss more like it!" Suddenly there is a shifting in her belly and she realizes that she is about to lay the eggs. "Hnngh!" After a few minutes of pushing the first egg comes out with a wet pop, Samus doesn't have any time to rest as the second egg gets into position and after more pushing, it too comes out. This repeats once more and she is left with 3 eggs. She instinctively curl them into her embrace before letting out a long sigh and falling asleep.