Chrysalis Syndrome is a condition in which a Looper Awakens for the first time in a variant of their home Loop. These Loopers treat this initial variant Loop as normal until it ends. Once they Awaken in a baseline Loop, they experience difficulty accepting which reality is their baseline and which the variant. Unlike Disassociative Loop Identity Disorder, they know intellectually what their Baseline is, but they retain a strong emotional attachment to the variant they first Awoke in.

The syndrome is named after Queen Chrysalis of the My Little Pony loops. Chrysalis first Awakened in a variant loop in which Celestia legalized and enforced slavery. In that Loop Chrysalis was legally married to Shining Armor and with him operated an underground railroad to get escaped slaves to safety. To this day Chrysalis occasionally pines for that Baseline.

The condition itself is minor enough that it went largely undocumented since the earliest generations, and many who first Awoke to alternate timelines did so because of the actions of their local Anchor. Ron and Hermione for example first Awoke to a Loop while Harry was playing Dark Lord out of boredom. Perhaps the most consistently awkward manifestation is when a new looper Awakens after being the subject of a 'One Loop Stand' from an existing looper who was looking for a temporary relationship, such as Vee (as well as a few incidents the Original Seven prefer not to talk about).

This syndrome has been noted in several cases during the event known as Hurricane Billy: the sheer quantity of crashed variant Loops resulted in substantial damage to Yggdrasil and the awakening of various parties which would not otherwise have begun looping. Of particular note is Gendo Ikari, whose son, Shinji, was replaced by Billy during his formative loop. While not suffering from Chrysalis Syndrome for long, he continued to use it as a convenient masquerade in order to keep Shinji seeing him as the villain.

The syndrome is one of the more stable conditions a looper can suffer from, and many can actually continue long and happy existences if there is little overall conflict without changing what they consider their 'original' self.

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