If you're working on unlocking all of Nier Replicant's endings, then you'll need to make sure you've collected every weapon in the game. Endings C, D, and E aren't available unless you've completed the chore, and getting there requires completing a few extra quests and trips to shops.
The Magical Stone is one such quest that rewards you with a weapon, just keep in mind, this one isn't totally necessary to grab the Iron Pipe, but it does a neat little trick in taking you back to the area from the game's opening cutscene. You'll also pick up 10,000 gold, which will come in handy for buying weapons later.
Keep in mind, this quest is only available after you've retrieved all five Key Fragments needed to enter the Shadowlord's Castle in the second half of the game. If you choose to forgo finishing The Magical Stone, don't sweat it. You'll automatically receive the Iron Pipe for completing Ending B.
How To Complete The Magical Stone Quest
To begin The Magical Stone, make your way to the Forest of Myth after completing your quest prerequisites. There, you'll encounter a Fortune Teller near the entrance of the area, she tells you about her plans to start a business, but needs a little help. She's waiting on a rare stone delivery that hasn't show up yet, but thinks Popola may know something about said stones. So, head back to Nier's Village and speak to Popola.
Popola knows exactly what you're talking about, the Eye of Power. She suggests going to the Lost Shrine to look for them on the roof, so take the ferry there, after you wrap up your conversation.
Make your way up the floors of the Lost Shrine, all the way to the top where you're outside and surrounded by decaying walls. The first moveable stone you encounter should be pulled back so you can jump into the area blocked off by the adjacent wall.
Pull the next block inside the enclosed area towards the right, up against the rubble on the ground. Run along the roof towards the back, you'll wipe out a group of Shades before reaching one big Shade. Destroy the creature, and it will drop the Eye of Power - you're now done here. Bring the stone back to the Fortune Teller in the Forest of Myth.
She'll ask if you want to have your fortune read, agree, and you'll be transported back to somewhere rather familiar. Run inside the building, where you were at in the beginning of the game, and destroy the crate there. The one-handed Iron Pipe should drop, pick it up and defeat the Shades.
When you're done, the Fortune Teller will give you one more reward, the 10,000 gold, marking the end of the quest.