Two endings achievable by losing the fight with the Eva Series. The first is a short cut scene where the bridge staff blow up HQ. (I obtained it in Misato's scenario.) The "Seele Wins!" ending is more notable and notorious. Since the game's "good" ending involves a successful Instrumentality, this ending is tasked with providing an outcome that is somehow worse. I don't think it went about this in the best way it could have, but... well, come to your own conclusions.
The minimalistic presentation makes NGE2 enigmatic even by Eva standards, so this sequence is rather perplexing, but fortunately there is additional context to elucidate things. Make sure you check out the Good Ending (also subtitled by me on YT), and especially read through the Classified Information (off the EvaGeeks site ONLY, since this is the version of the translation that I personally maintain).