If entering the boss room without Zora Armor, either put on the Iron Boots before entering the load zone or as soon as possible after gaining control of Link in the arena so that Link has enough air to reach the fight trigger. If Link swims without the Iron Boots before starting the fight, it is safest to return to the surface of the water, wait for the air meter to disappear from the screen, and then begin sinking.
With Master Sword, it is possible to 1-cycle this phase and skip the bomb fish emerging simply by quickspinning or jump attacking the eyeball. After doing so, swim with water bombs but DO NOT hold a direction. This will cause Link to float up high in the arena during the mid-fight cutscene. Link will not float up if the player fails to unequip the Iron Boots or swims in a direction with the water bomb rather than leaving the control stick neutral.
Clawshotting Morpheel's tentacle just before sinking into the cutscene, will prevent the cutscene from playing, making it possible to clawshot the eye immediately. Note that this does not refill the air meter, so this will cause Link to drown without the Zora Armor.
Note: Before the cutscene for the 2nd phase starts, using the Clawshot will rocket Link up to the top of the arena and make him drown without Zora Armor.
After clawshotting onto Morpheel and attacking four times, let it buck Link off. Immediately start swimming up and left until it is possible to clawshot back on. Morpheel will always go up-left after throwing Link off unless the wall of the arena is in the way.
It it possible to regrab Morpheel nearly instantly after completing a cycle, which saves time with or without Zora Armor. Put the Iron Boots on before clawshotting onto Morpheel's back, and after dealing damage, force unequip the Iron Boots by equipping another item on their button. This will cause Link to fall off of Morpheel without the bucking animation. Morpheel will continue to swim away, but it is now possible to regrab Morpheel by clawshotting very quickly before she gets too far away.
Notes on regrabs:
If Morpheel's head segment is below horizontal when shooting the clawshot for a regrab, then the regrab will usually work, and if it is above horizontal, the regrab usually will not work. While the item wheel is up for the Iron Boots force unequip, check the head segment's angle. If it is horizontal and on its way down or is already down and not near horizontal on its way up, then it will likely be at a good angle when clawshotting immediately after closing the item wheel. If the head segment is not at a good angle when the item wheel is up, close it without force unequipping and pull it up again to find a good angle. The angle of the rest of Morpheel's body does not matter for regrabs.
If Morpheel makes a sharp turn as the player goes for a regrab, then the regrab will often fail.
If pieces of a pillar that Morpheel destroyed are falling as the player goes for a regrab, then the regrab may fail as Link gets pushed around.
Morpheel's head shakes 3 times before Link is ejected. If Link is ejected or the regrab fails, go for another normal grab (with Zora Armor) or sink to the bottom to refill the air meter (without Zora Armor).
In most RTA cases, the ideal Morpheel fight without Zora Armor will use two water bombs for air refills. Failing to force unequip the Iron Boots in time for the mid-fight cutscene, failing a regrab, or being ignored by Morpheel when swimming up after the 2nd air refill will cause the fight to require more bombs.
When the mid-fight cutscene ends, hold target, leave the control stick neutral, and equip the Clawshot and Iron Boots. Toggle the Iron Boots on and off to track Morpheel's height in the arena, erring on the side of being higher than Morpheel. Press A to drop the bomb and refill the air meter before the bomb explodes (and before the air meter runs out, which can be a concern if Phase 1 did not go smoothly). Approach the top of Morpheel with some combination of sideways swimming and Iron Boots tap swimming.
Equip Iron Boots and clawshot onto Morpheel's back. Hit the eye four times with B and then force unequip the Iron Boots to get off without waiting as soon as the red flash from the fourth B attack is visible. Sink to the bottom of the arena.
Shortly before it looks like Morpheel is going to turn and swim towards Link, swim with water bombs again. This time, hold a direction during the trick to help position Link where Morpheel is headed. Press A to drop the bomb and refill the air meter before the bomb explodes (which occurs just after the 7th red flash) or the air meter runs out, then swim sideways and/or up (mashing A) to get Morpheel to aggro and begin the sucking animation. If anticipating Morpheel being too high to aggro, sink to the bottom and try again.
Swim sufficiently above Morpheel, put on the Iron Boots, and clawshot onto its back. After dealing four blows with B, regrab Morpheel as described in the Regrab Tips section above (without Iron Boots on) and press A to deal the final blow.
Being sucked in by Morpheel deals 1 heart of damage to Link. With a nearly full air meter, it is possible after being sucked in to swim upwards and continue with the grab and regrab to end the fight as normal. With less air, it can be better to go for a grab without a regrab or to abandon the grab and sink to the bottom for another attempt. Morpheel cannot suck Link in when he has the Iron Boots on unless the player puts the Iron Boots on on the last possible frame before the sucking cutscene begins.
Pressing A on the final cycle does not end the fight immediately, so the air meter must still be partially filled after the regrab to avoid drowning between pressing A and Morpheel's death cutscene beginning.
With good air management and good swimming RNG from Morpheel, it is possible to finish the fight using only one water bomb to refill the air meter. This saves around 15 seconds versus a good Two Bomb, but it is very risky, as failing the second regrab will usually result in Link drowning.
After jump attacking or quickspinning the eye in Phase 1, pull the water bomb as late as possible before the mid-fight cutscene begins so that there is as much time left on the bomb timer as possible at the beginning of Phase 2.
Once the cutscene ends, delay pressing A to drop the bomb and refill the air meter until just before the bomb explodes. If Morpheel's swimming RNG brings it close enough to Link that he can reach its back as the air meter is appearing on screen or before, then there is enough air left for One Bomb.
As in Two Bomb, put on the Iron Boots, clawshot onto Morpheel's back, strike the eye four times with B, and then force unequip the Iron Boots. Instead of sinking to the ground, re-equip the Iron Boots, put them back on, and regrab Morpheel.
While everything in the Regrab Tips section above still applies to this regrab, the air meter is so tight for One Bomb that it is arguably not worth pulling the item wheel multiple times to try to find a good head segment angle, as each item wheel pull costs air and time. It is safer to attempt this first regrab as soon as possible; if successful, proceed with One Bomb, and if unsuccessful, proceed with Two Bomb.
If the regrab is successful but Morpheel turns sharply, it can take Link a long time to actually reach Morpheel's eye, which takes time and air. If this happens on the first regrab in One Bomb, it is safest to force unequip the Iron Boots immediately (without striking Morpheel's eye), sink, and proceed with Two Bomb.
Strike Morpheel four times with B, force unequip the Iron Boots, do a standard regrab without the Iron Boots on, and press A to deal the final blow. If Link reaches Morpheel's eye before the air meter turns red, then there is enough time to finish the fight without drowning.
During Phase 1, if Morpheel lowers a tentacle to grab Link, the player can strike the tentacle to make Morpheel retract it. However, if the tentacle is struck on the same frame that it grabs Link, then it will retract, but the eyeball will be invincible for a short time and will teleport back into Morpheel as soon as its invincibility ends. If this happens, refill air and then redo phase 1 as normal.
During Phase 2, clawshotting onto Morpheel's back during its sucking animation will cancel the animation. However, when clawshotting onto Morpheel while it's swimming, it is possible for Morpheel to begin the sucking animation mid-clawshot and continue it while Link is attacking the eyeball. If this happens on cycle 3, pressing A will cause the entire final blow animation to play but will not kill Morpheel. It is likely impossible for this to happen on a cycle that begins with a regrab.