Ender 3 Distorted Calibration Cube
Resolution: After many trials and errors, I finally replaced the nozzle with one that that was not partially blocked by filament at its entrance. 



Likely cause: A careful examination of the old part hints, that the repeated blockage in the nozzle seems to have been caused by a gap between the PTFE tube and the nozzle, which has considerably moved backwards under the stress of printing as one can see here in a photo of the PTFE tube.



It took me about a month and I went down a few rabbit holes until @user77232 made a great suggestion to check the nozzle and see if it needs to be cleaned. Thanks for helping me out everyone!