Yumi went there by herself.

Literal

Yumi [topic-は] one-person-[with-で] there [to-へ] go-[past-った].

一人で ('alone, by oneself,' literally 'with one person') uses で to mark the manner/means of doing something. Note that 一人 here isn't counting people — it's the adverbial 'alone.' Parallel constructions: 二人で ('the two of us, together'), 家族で ('as a family, all together').