Autoimmune cross-targeting hypothesis: a virus marks the inside of a cell while a larger infection marks the outside and the combination triggers autoimmune disease. The immune system is instructed to destroy both the inside and the outside of the target.

Narcolepsy has been considered as autoimmune possibly triggered by infections but the focus was on molecular mimicry
http://www.ncbi.nlm.nih.gov/pubmed/21963829

The dorsal raphe nucleus cells would be the target for Narcolepsy and the inside of the cells would be marked by the flu virus while the outside would be marked by the strep.

Narcolepsy and strep
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2786037/
http://www.ncbi.nlm.nih.gov/pubmed/23493659
http://www.ncbi.nlm.nih.gov/pubmed/19725248

Narcolepsy and the flu virus H1N1
http://www.ncbi.nlm.nih.gov/pubmed/24559657
http://www.ncbi.nlm.nih.gov/pubmed/24551456
http://www.ncbi.nlm.nih.gov/pubmed/26216616
http://www.ncbi.nlm.nih.gov/pubmed/24849861

Hypotheses: Autoimmune Cross-targeting, Co-carcinogenesis, and Quorum complications