。
She was afraid he might be feeling lonely and forgotten.
Literal
She [topic-は] [he [subject-が] lonely-feeling and is-forgotten [end-up-てしまう] [is it not the case that-のではないか]] [quotative-と] thought [explanatory-のです].
A densely embedded sentence. The inner clause stacks 寂しく思い ('feel lonely,' with 思い in stem-form linking to the next clause), 忘れられて ('be forgotten,' passive te-form), and しまう (the regretful/complete auxiliary). The whole proposition is then framed with ~のではないか — a worry pattern, 'I'm afraid (it might be) that ~.' The closing ~のです gives an explanatory tone.