To me, Annihilation was more of a Philo-Fiction than a Sci-fi. I have to introduce a philosophical view to explain it. German philosopher Martin Heidegger saw all of existence, including- living beings, inanimate objects etc., as negation of ‘Nothingness’. If you consider an empty glass- even if there is no water, the glass is still there. Considering pure vaccum, there is still the container. To him, Nothingness is the original state of everything. We are in that sense negation of a certain ‘Nothing’. The Nothing I am talking here may or may not be something like Dark Matter or Dark Energy, but I leave the physical interpretation to you.
The ‘Shimmers’ place may have contained a different kind of ‘Nothing’ than that of our own. Did you notice how the light also had a strange glow? The new ‘Nothing’ acted like a prism made by a medium placed upon another, which refracted DNAs of different species like refracting light. Evident by the crocodile having teeth of shark, the surreal bear preserving the dying part of its victims’ minds, the human shaped plants, finally the overall DNA mixture of the human characters from the time of entrance. When at the end Lena (Natalie Portman) asks if Kane was ‘Kane’, he replied no. I think, so wasn’t Lena.
There were Buddhist themes present in the film also. Like lives transforming from one form to other, shown by the uncanny event of the bear preserving dying mind as mentioned earlier. Only beings willing to embrace ‘Nothing’ through self-annihilation achieve Nirvana, as did the formed beings mirroring humans entering the light house. May be the final annihilation of the whole Shimmer place represented the new ‘Nothing’ diffusing with the original.
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The movie, Annihilation had a very unique theme, as opposed to the territorial alien invasion Sci-fis. When the investigation team asks Lena if there were any aliens left, she gave confusing answers – because there weren’t any alien life forms present in the first place. The new ‘Nothing’, to me, remained in a difused form with the original.