Naive question, possibly poorly formed: what is the purpose of the parts of the plant? Eg the leaves are for collecting energy and the flower for reproduction...so is the "thing" that all that work is going to benefit really just the root stem?

The answer to pretty much every biological "why" question is: because it reproduced. It seems simplistic, but really, a thing is here and alive because its ancestors reproduced.

Your version of the question has surprising perspective- I think you are asking what the "it" of the plant is. That's an interesting personification of a plant. I think it points to the fact that plants may be safer underground- for anchoring, for not being eaten, for getting shielded from harsh elements.

Isn't reproduction the point? The roots exist to obtain water, nutrients, minerals; leaves gather energy from the sun; this is used to grow fruit, or whatever is used for reproduction