Yes it's plagiarism in the sense that you, yourself, describe. You write, "..by citing his sources that he found, while ALSO citing the Graduate thesis itself as a source
indirectly." If you are are providing an indirect citation you must at least provide in a footnote that the idea you're expressing is not your own, but the writer's being cited. If your indirect citations comprise the bulk of your paper, then it is apparent the paper is not
yours, but that of the author being cited.
Btw, I have done graduate level work, and am still doing so. I am half way through my master's degree, so this is pretty fresh in my mind.
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EDIT: Here is the APA standard for indirect citations which may be helpful.
If you use a source that was cited in another source, name the original source in your signal phrase. List the secondary source in your reference list and include the secondary source in the parentheses.
Johnson argued that...(as cited in Smith, 2003, p. 102).
Note: When citing material in parentheses, set off the citation with a comma, as above. Also, try to locate the original material and cite the original source.
https://owl.english.purdue.edu/owl/resource/560/03/