Dice the onion and peel, deseed and chop the squash in medium-sized chunks.
Heat butter in a wide pot/pan over a medium heat. Add the onion and cook, stirring occasionally, for around 2-3 minutes until starting to soften.
Meanwhile peel and chop the apple and finely chop the sage.
Add the squash to the pot and cook another 3 - 5 minutes, then add the apple, sage and thyme and a little salt and pepper. Cover, reduce the heat slightly, and let the ingredients sweat a few minutes.
Once the squash and apple are starting to soften, only a few minutes more, add the flour to absorb and excess fat, then add the stock.
Cover and bring to the boil then reduce to a simmer. Cook for around 10 - 15 minutes until the squash is cooked through - it should be tender to the knifepoint.
Remove from heat, blend the soup with an immersion blender or transfer to a large blender (if you transfer, take cake to let it cool a few minutes first as it should not be too hot when placing in a blender. If needed, reheat after). Serve or store until needed - it re-heats well.
Video
Notes
I find the easiest way to blend soups like this is with an immersion/stick blender (affiliate link).