You have a pretty interesting idea of plagiarism... Pretty sure if the dude talked about how he retrieved the DRAGON STONE for the COURT WIZARD of WHITERUN it's plagiarism, pretty clear cut. Still funny, though.
No, it is not. There are many things that can and will happen along the way and the words "dragon stone" and "court wizard" do not make it a plagiarism. Nor will the use of words like "Pepsi" or "Coke" make a story a plagiarism. And if a painter uses only certain colours and motives and I choose to use these too does it not make my work a plagiarism either.
How a player manages to get the dragon stone is not predetermined and therefore is there no plot that can be copied. The events of the story will unfold differently for every player. Some will play as a Khajiit and others as a Dark Elf. Some as a warrior and others as a mage. Some will encounter a deer, others a wolf, for some will it be night and for others will it be day, and so on.
I would be more worried if the OP had used all of Skyrim's quest lines. Or the quest line of a game like The Witcher II, which only pushes you from stage to stage and where you cannot go back. Then there would be too little variations and the risk of committing plagiarism becomes high. Yet, it would not be impossible to write a unique story within the world of The Witcher and one that has got little to do with the game's plot itself but only took place at one stage.