Here in the bottom there is a little bone which defines the base plate movement , kind of ankle:
Problem is: It is not joining or connecting or parenting the other bone joint. I tried head-tail direction flipping also. Whatever I tried did not work.
Any idea would be appreciated…
Hi. I my be stating obvious here but I’ve had similar conundrum some time ago. I can see you are in pose mode. What I had to do with mine was to join them in object mode (Ctrl+J) so they are as one object. Than create parent in edit mode. I’m not sure you can parent bones in pose mode. Hope it helps
Hi, thank you for your response but they are already in same armature so I cannot join in object mode. I tried in both, edit and pose mode, neither worked…
Is there a hierarchy in the chain? I first started building upper side and at last I added that little bone. If there is something like “root” or “bottom”, maybe it is the reason?
From the manual: " The bone at the beginning of a chain is called its root bone , and the last bone of a chain is the tip bone (do not confuse them with similar names of bones’ joints!)."
I guess it is not allowing branching from the very bottom, it is needed to split bones from the tip of the root bone. 
Not sure how are you making this. Normally if I wanted to add your small bone as a root I would select your big bone from the upper chain in Edit mode than shift select small “root” bone so its the active one and than Ctrl P. Click keep offset if you wanted to and now you should be able to move everything using Root bone in Pose mode. If You click “Connected” it will than move entire chain to the thin part of root bone. To avoid that you can position your root bone first. By vertex snapping in Edit mode. Select head of your root bone and snap it to bottom of your chain bone on the thick bottom end.
Yes, I had found it too just a minute ago, so that way we are able to change the root. It is simple but took me long to figure it out… Thanks…
This things are like that. Sometimes you stare at it and cant see it for hours. And once you find solution it seams so obvious.
Well done for keeping at it. Glad I could help
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