Is it plausible that eukaryotic organelles like flagella and cilia are the result of endosymbiosis with spirochetes?
Well, since all cells in a multi-cellular organism originally come from the same precursor cells, it’s hard to argue that some of them have endosymbiotic compartments that are missing in others, and notably their precursor.

Notably, there are species which possess both ciliary and rhabdomeric photoreceptor cells, and their precursor is non-ciliary. This is incompatible with Margulis’ endosymbiosis hypothesis.

PZ Myers has a good summary of the relevant papers [1, 2].


[1] D. Arendt, K Tessmar-Raible &amp; al., Ciliary photoreceptors with a vertebrate-type opsin in an invertebrate brain, Science 306, 2004.
[2] D. Arendt, Evolution of eyes and photoreceptor cell types, Int J Dev Biol. 47, 2003.