Annihilation ending explained

What happens

Lena destroys the entity that copied her and escapes as the Shimmer collapses. Afterward she is reunited with the man who returned as Kane. He admits he may not be the real one, and when they embrace, both their eyes briefly shimmer.

The last image

Lena and the returned Kane embrace, and for a moment both their eyes shimmer with the zone's light.

Three readings

1 · Both were replacedThe shimmer shows that Lena, like Kane, is now a copy, and neither knows it.

2 · Both were changedThe zone altered them, but they are still themselves, only different.

3 · Deliberately unanswerableThe film wants you to feel that you can't tell, and that no one could.

What it says

Change in the zone isn't good or evil, just unstoppable. By refusing to say whether Lena is still herself, the film asks whether a self can survive change at all, and whether a perfect copy matters.