There's a few questions here, so I'll break it down a little.
The best way to determine what finishing regimen you should use is to make test boards with different steps until you can produce the finish you want. Take a scrap from the project and do whatever sanding, sealing, coloring, and top coats you think you want and see how it looks. If it's not right adjust it. Also, keep in mind there are really no hard and fast rules as to what you have to do with finishes (other than making sure preliminary layers are cured before covering them and watching out for incompatible products). Experiment and see what you like.
In the refinishing space your options are a bit more limited, but there's almost always a non-show surface. You mentioned door, so I'm assuming you mean an entry door, not a cabinet door. You can use the top, bottom, and hinge edge for testing. If you need more tests you can sand/scrape/plane them back and try again.
Should I stain or just use poly?
Stain is intended to change the color of the wood. It is typically used when you have a less expensive lighter colored wood (i.e. pine) and you want to make it look like a more expensive darker wood (i.e. walnut or cherry). It is certainly not required, and many woodworkers avoid it entirely. If the wood is coming out of the finishing procedure the color you want then don't bother with any stain. If you do want to change the color I'd actually recommend an analine dye in alcohol over a stain...
What color should I use?
What color do you want it to be? This is totally subjective and depends on your vision for the piece.
Natural stain is just another color. Like any other stain it will change the wood to be closer to the color of the stain. It is not intended to "leave the wood a natural color". If you like the color of the wood don't use any stain.
What kind of poly should I use?
Generally there are two broad categories of poly, oil-based and waterborne. Waterborne cleans up more easily and doesn't impart much color to the wood. Oil-based requires solvents to clean up (mineral spirits, turpentine, paint thinner) and tends to make the color a bit more amber.
Do I have to recondition?
You don't have to use any kind of conditioner if you're not using a dye or stain. Conditioners are mainly to prevent "blotchiness" when staining by blocking the more absorbent parts of the surface so they don't suck up more colorant and appear darker.