"R.I.P. YogCave. Never Forget."
The site that would become the YogCave was discovered in Minecraft - Part 3: Moving into the Yogcave after Xephos and Honeydew departed Simon's Shack in search for coal, as to prevent spending another night in the darkness. After harvesting a vein of coal beneath a cliff face in a natural cavern, they evaluated that the said cavern offered adequate defence against hostile mobs with its natural formation, not to mention being quite spacious. This motivated the duo to settle into this new location.
Honeydew returned to his temporary shack and demolished it for its materials while Xephos dug a layer of dirt out of the floor to use as building material. They spent the majority of the day sealing up the entrances to the cave to prevent entry from monsters and were able to complete the project by nightfall.
Even before it was destroyed, the YogCave had gone through some tough moments in the series. It was the scene of direct attacks by Israphel on two different occasions and suffered another sneaky attack by him when he rigged the back entrance with a skilful trap of TNT. It has also been subjected to flooding, and Honeydew's 'accidental' burning of the floor in an attempt to turn the heating on.
The YogCave was originally a natural cavern set beneath a cliff-face. In Minecraft - Part 3: Moving into the Yogcave, after spending their first night in a hastily constructed shack, Honeydew and Xephos begin hunting for coal which leads them to the site of the YogCave. As the coal is mined and the cave dug out some more, the guys decide to move in because of the structures natural defences (Namely a load of stone and dirt protecting them on several sides).
The first modification made to the natural cave is the addition of dirt walls and a dirt ceiling in Minecraft - Part 4: The first quest! Pork and Glass, to prevent hostile mobs from spawning and attacking them at night. Gradually the cave is improved until it begins to resemble a real building. By Minecraft - Part 5: The Legend of Pig Island it receives a wooden floor, doors on the front and back, and several windows. Around the same time, a mysterious tree appears immediately outside the front entrance, plus the TNT trap which kills Honeydew and takes out the back wall can also be seen. The trap was probably put down at the same time the tree appeared.
One of the first major exterior changes comes about when Xephos decides he wants to build a massive tower extending out of the mountainside.
In Minecraft - Part 10: "Renovating" the Yogcave, the endurance of the YogCave is put to the test for the first and second times. The first test comes when Honeydew attempts to "put the heating on" for Xephos as the latter is arriving home from harvesting pork in the dark. The result of this act is a semi-wild fire breaking out and destroying approximately half the floor. It is at this time that the first modification made by Israphel is discovered as well, in the form of a shaft in the middle of the floor.
Mere seconds after the fire is put out, another large chunk of the YogCave is destroyed when Honeydew goes to check out the back door, steps onto a pressure pad, and sets off some hidden blocks of TNT, killing himself (again) in the process. The pressure pad can be spotted as early as Minecraft - Part 6: The Mysterious Tree, set up so that it could only be stepped on if one exited through the door, so as to not be set off by wandering animals or monsters. Despite these setbacks, however, the YogCave is restored and improved with a new wooden floor and a pool with a mossy cobblestone bridge where the back door used to be.
The next major change comes when Honeydew and Xephos decide they need to go mining and dig parallel mineshafts down to bedrock going out the back of the YogCave. The shafts eventually connect to a natural cavern which leads the duo to discover treasures such as obsidian, gold, redstone, and diamonds. Triumphant in their quest for valuable goodies, the two return to the surface and leave the cavern open for exploration later if they decide they need more.
Not much changes about the YogCave until the first video after the upgrade to Minecraft Beta when Xephos, while detailing all the things they can now do in Beta, mentions offhandedly that "there's a sign on the door which is incredibly creepy." The sign is, in fact, a note from none other than Israphel himself, telling Honeydew and Xephos "You should close the door." This is a reference to the fact that both characters, particularly Xephos, have a terrible habit of leaving the doors open behind them and allowing things such as creepers, Daisy the Cow, and chickens to get inside their house. Other modifications courtesy of Israphel are discovered at this point, including a waterfall by the front door presumably designed to knock hostile mobs away, and another note on the back door which reads "No traps this time. Promise.".
The final major intentional change to the YogCave comes when Xephos decides he wants to build stairs up the side of his tower to the top of the mountain. Having successfully built his set of "terrible switchback stairs", the two set to work installing upper floors and windows in the tower when they are again attacked by Israphel. As he runs away, our heroes give chase and end up not returning to the YogCave until Minecraft - "Shadow of Israphel" Part 1: Crash and Burn.
After being rescued from Survival Island by Old Peculier and Skylord Lysander, Xephos and Honeydew finally return to the YogCave only to find it in ruins. Not only the YogCave, but the majority of the mountain from which it was built had been destroyed. The only remaining intact parts were half of the floor (ironically, the same half that Honeydew previously destroyed in Minecraft - Part 10: "Renovating" the Yogcave), a door, and the waterfall installed by Israphel. Part of Xephos' tower remained standing, though it was so full of holes it no longer had any useful function. It was mentioned during the one-off episode for PAX that the Yogscast, when done with Shadow of Israphel, might upload the world as a map, with challenges such as rebuilding the YogCave.
Since the horrific destruction of the YogCave, Pimp My Minecraft have managed to not only rebuild it, but have also added many new rooms and features. These include a jacuzzi, a giant stone statue of a woman in a golden bikini, a cookie dispenser (with signs saying jaffa cakes), lights that come out of the floor, a study area, and behind some bookcases, a cannon used to fire TNT at a replica of Israphel's face.