According to Freud, Destrudo is the manifestation of Thanatos, the death instinct. Just as Eros, is the life instinct, and it has Libido, the sex drive, the desire to live out the life instinct, Thanatos has Destrudo. The death instinct has the death drive. It is the desire for death, for all things destructive, it is the way in which our Thanatos affects us.

Update 19/04/01

In episode 26', when Makoto Hyuuga checks the status of Eva-01, he confirms that the Destrudo of the pilot – Shinji Ikari -- is materializing. Destrudo is the energy of the self-destructive impulse advocated by E. Weiss. It is the antonym of Libido. It is different from Mortido -- the energy of the "Death Instinct" advocated by P. Federn, the mentor of Weiss.

Source: The End of Evangelion : Glossary contained within The End of Evangelion - Theatrical Program.

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