I hope the carcass of Sapphire Weapon will be visible from your perspective when approaching the Underwater Reactor and when you leave at the start of the submarine section.
One thing I only just now realized is that I've long held the headcanon that Weapon can't die but that they only go to sleep and regenerate, unless some big planetary force (like Holy) tell them to stop being active. It's a probable misreading of what Ifalna says in the tapes at Icicle Inn.
PS1, Japanese line:
「ウェポンが消えることはありません。
…この星のどこかで眠っているのです」
PS1, English line:
“Weapon cannot vanish.
…it remains asleep
somewhere on the Planet.”
The line is in response to Gast asking “
So, Weapon no longer exists on this Planet?”, so Ifalna may simply be stating that Weapon don't just disappear on their own, stating nothing about their regenerative capabilities.
Since Omega Weapon is part of the planet's whole cycle-shindig I reckon that particular one is effectively immortal and will simply regenerate when the time is right, but I'm not sure how to view the five anti-Jenova Weapon (Sapphire, Ultimate/Ultima, Diamond, Emerald and Ruby).
All this speculative interpretation aside, I wouldn't put it past Square if they changed the Underwater Reactor scenario so that Sapphire Weapon started to regenerate and that it had to be quelled with submarine missiles to postpone its re-awakening. I hope they don't go that route because it would diminish the satisfying impact from the Junon cannon blowing Sapphire Weapon's head off, though admittedly depicting Weapon as an eternally regenerating zombie would make them a bit scarier as threats.
Is anyone hoping that Ruby- and Emerald Weapon will be integrated into story scenes? With the Remake generally turning the dial up to eleven it seems tempting to include Emerald Weapon somewhere in the Underwater Reactor scenario. By nature of it being a mako reactor it definitely makes sense as a target for EW to focus in on, destroying the reactor and some Shinra subs and nearly taking our protagonists down as well.
Story-wise I don't think we need to see each planetary Weapon definitively defeated in the main, obligatory narrative. There is something to be said about optional super-bosses remaining undisclosed as to whether they were defeated in the narrative or if the victory over them *only* exists in gameplay. But I am tempted to see the Weapons, particularly Ruby and Emerald, integrated into story scenarios.
Should Ruby Weapon emerge and tear down the Gold Saucer, forcing the money-drenched Dio to face the angry inhabitants of Corel Prison after he's crash-landed on the ground? Should this somehow be integrated into the North Corel scenario with the Huge Materia? Many options that are at the risk of bloating- and dragging the story, but interesting possibilities nonetheless.