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Unlike most movies that have an black backdrop during the credits, the Heisei Godzilla films had special footage that played during the credits. In this film we see the symbolic image of a rose above Earth, showing audiences that Biollante is still alive and a possible hint to her return to Earth in "Godzilla vs. SpaceGodzilla".

Yes, in fact there are three. keep in note these scenes can not be seen on the internet anywhere (as far as I have searched) or on the Sony Tristar DVD release of the film. In order to see them you must buy the actual Toho DVD

1) Extended footage of Godzilla marching to Lake Ashino

2) At the end of Godzilla and Biollante's first fight, he kills her as he did in the final cut, by setting her on fire with his heat ray. However, in the deleted scene, the golden energy spores left behind her body rise into the air and then cover the shores of Ashino lake in a blanket of beautiful flowers. godzilla is only briefly intested, before leaving. Although Koichi Kawakita (the SFX director) was impressed with his work, the flowers were out of scale, and so the screen was scrapped.

3) there was a radical alternate ending where Godzilla actually dies from the ANEB (Anti-Nuclear Energy Bacteria) and Biollante, also wounded due to Godzilla's heat ray, swallows Godzilla and both become the golden energy spores seen earlier when Biollante first died. The scene used a combination of anime and live action to depict this, but this was ultimately cut out in order to continue the series . Godzilla died a somewhat similar death six years later in the film "Godzilla vs. Destroyah"

4) There is a famous cut scene where stop motion is used for the first fight scene between Godzilla and Biollante, but this was cut out because it didn't match with the rest of the film.