If the whales hadn't gone extinct the whale probe would have no reason to show up.
If the whales were hunted to extinction in the Prime Universe, you really think the same didn't happen in the Mirror Universe? Or did the Mirror Whales fight back until eventually an uneasy accord was struck between human and whale?
Good question.
But why did the humpback whales go extinct in 1986?
Natural Selection through being hunted by man? Not very likely.
There is a 300 year span Between 1986 and 2286, the timeline of Star Trek IV. The Vulcans had made contact with Earth in 1957, some 29 years prior to Kirk and Crew traveling back in time to 1986. Which was some 329 years prior to the Whale Probe arriving at Earth. The Vulcans were intrigued by Sputnik and began to investigate, Carbon Creek : Ent. The Enterprise also went back in time to 1969, TOS: Yesterday is Tomorrow, which was 12 years after the Vulcans became intrigued with Earth and 17 years prior to the HMS Bounty arriving in 1986. Kirk also mentioned to Captain Christopher that he had 'better hurry,' as he only had 15 years. What took place in 1984 or 15 years after Yesterday is Tomorrow? Two years later Kirk and crew show up looking for humpbacked whales in 1986. Did the Vulcans detect the Enterprise in the Sol System in 1969, which was the first year that humanity travelled to the Moon? An event that the Vulcans would most likely have been monitoring since 1957 after becoming intrigued Sputnik. It appears that small shiny things seem to attract the Vulcans the best. In 2063 Zephram Cochrane made his first warp flight that attracted a Vulcan survey ship that had just been 'happening through' the solar system. For 106 years the Vulcans would have in fact been watching and surveying Earth, after being intrigued by the Earth developing their space program so rapidly.
What I am getting at is this, the whale probe didn't show up for 329 years later? At max warp possible, how far would the probe have traveled in 329 years?
I seriously doubt that animal conservationists would have allowed humpback whales to be hunted to extinction. Or was the hunting of the whales extinction part of the alien Threat Force's incursion into the past hoping to draw the whale probe to Earth, some 329 years later? Could it be possible that a threat force from the future, an enemy of the Vulcans who was watching the Vulcans watch Earth, went back in time and killed off the Humpbacked Whales knowing that the Whale Probe would come to inquire about their disappearance?
Could the threat force alien species have known that the communication methods of the Whale Probe would destroy Star Fleet HQ where such destruction would have allowed threat forces in the ST:IV era to launch massive attacks against Starfleet after the Whale Probe had destroyed Starfleet HQ and returned to where ever it had come from?
What was so important for Captain Christopher to do in 1984, two years before Kirk and Crew arrived to save the last two humpback whales? Was Captain Christopher made into a Temporal Agent and sent back to Earth to do something in 1984?
Mirror, Mirror
In 2257, Michael Burnham travelled to a Terran parallel universe, Disco :The Wolf Inside, some ten years before Kirk did in 2267, TOS: Mirror, Mirror.
The
Red Angel was an entity sought by both Starfleet and Section 31 in relation to a series of mysterious
red bursts that occurred in the late 2250's. The Red Angel suit was a product of the Daedalus Project, a time travel program set up by Section 31 in the 2230s out of concern of a
temporal arms race with the Klingons.
From the highlighted section above, we can see that Star Fleet and the Klingons have been engaged in a temporal arms race since the 2230's or 27 years prior to the first Mirror, Mirror Universe appearing. Did the Klingon's create the Terran mirror Universe to trap Burnham and Spock in?
Or
Were the mysterious red bursts detected in 2257 or 2259? The red bursts being detected in 2257 after the Red Angel had been used would be open the door to Burnham possibly being the central starting point of the Terran Mirror Universe. After all Burnham was able to use Red Angel, therefore Red Angel could have tapped into her and transported her to the Terran Universe along with Spock, ten years later. There is a vague connection between Burnham, Spock, Red Angel and the Terran Mirror Universe.
Was it the Klingons who went back in time to 1986 to quietly try and kill the Earth off in the future by eradicating the Humpback Whales in the past that would draw the wrath of the Whale Probe 300 years later? Or could the Romulans and Klingon's both have conspired, together, to eradicate the whales in 1986 to effect the future of the Federation in their favor? After all, the Romulans and Klingons have been allies in the past. We also know that the Hur'q invaded Qo'nos, stole some Klingon artifacts and eventually went extinct but were only in hibernation. The Klingon's reverse engineered Hur'q tech and developed warp drive, which would have brought the Klingon's into contact with the Romulans sometime before 2230.
*An alliance between the Klingon Empire and the Romulan Star Empire formed in the mid-23rd century.
With the Hur'q being from the Gamma Quadrant and the Hur'q possibly traveling through the wormhole, the Hur'q could have encountered an alien species that had seen the future, the Burn and post-Burn era, and disliked how Starfleet and the Federation had proceeded and sought to destroy the Federation before it even got started.
Thus there could be some entity inside of the Bajoran Wormhole enlisted the Hur'q to invade Qo'Nos and allowed the Klingon's to capture Hur'q technology to become warp capable. Warp capable enough to travel back in time and effect the Federation's growth by eradicating the whales that drew the whale probe to Earth in hopes of destroying Earth and the Federation when the eradicated humpback whales did not answer. After all we do see the Klingon's destroying an ancient Earth probe in Star Trek V. Why would the Klingons be so interested in 'tracking space junk' unless they were actually looking to destroy any evidence of Earth's past, just like they tried in Star IV.
There is definitely some malevolent force inside of the Bajoran wormhole or on the other side of the Bajoran wormhole that may even be deeper than the
Bajor-B'Hava'el system in the Alpha Quadrant. A malevolent force that might be responsible for the timeline shifts and mirror Universes to try and eradicate key members of the Federation or prevent Starfleet from ever happening, where Disco has become the focal point in the entire war that Burnham has been unaware of fighting since the first mirror in 2257. A war that no one realizes they have been fighting except those on the other side of the Bajoran wormhole...