The analysis is always with respect to the work that the owner is claiming infringement of. Work C would be compared to work A.
The copyright owner would have to prove copying happened (even via an intermediary, like work B). The copyright owner would also have to prove that work C included a substantial amounttaking of the original work in A was included in work C.
The owner of work C could raise a fair use defense, and work C would be subject to the 4-factor fair use test in relation to work A.