Binge rationalizing - the next best thing after Ben&Jerry's.
...Is simply a cover story, as nicely explained by previous posters. Yes, L'Rell and Voq had an affair, but Tyler's body need not have been involved in it in any fashion. But Tyler being in the hands of L'Rell's faction ever since the capture at the Binaries is likely: this House did run a prison ship and was famed for its interrogators and all, and did have Starfleet prisoners other than Lorca and Tyler/Voq, the two that were specific pawns in L'Rell's games.
Whether House of Mo'Kai would keep a random human prisoner alive for six months is unknown. But Klingons do take prisoners, habitually (they just don't take hostages to protect their own skins, because that gets them slain for cowardice), and Tyler might have been the guy unfortunate enough to outlive his 123 compatriots. At least for the most part (that is, with sufficient body parts more or less intact).
I like that one. It's not so much the doing of the meld itself, but of Spock driving himself insane till a powerful telepath slaps him in the frontal lobe like any good Vulcan Healer.
Did she? We never learned there would have been a genocide in progress. What happened was that the Ba'ul had been told to cease and desist; they fired a set of red rays to their "pylons"; and lo, the pylons did cease to work.
Burnham Jr. just knew she had to be there so that Saru could see her. She didn't need to actively do anything with that suit, which for all we know did not have the optional extras and accrued goodies of Burnham Sr.'s suit.
...What's the problem there? SF already had basic intel that Klingons were geologically vulnerable to such bombing, and if they did not, Tyler would have provided some, and if he did not, Emperor Georgiou would have been familiar with the innards of all things Klingon, be it conquered homeworlds or cut-open warriors.
That the plot then could be turned into the blackmail scheme is the harder pill to swallow. But we saw the aftermath and could appreciate that the Klingons craved a leader, any leader, under any pretext. L'Rell just had to posture louder than her competitors - and those competitors clearly saw advantage in letting one fool try first before they would step in and take the reins. After which it was standard Klingon backstabbing politics all the way.
Most Trek superbeings can. Some choose to look vaguely humanoid, but few are indicated to actually be that. Probably it's no more curious than the ability to do calculus is to us, or the ability to use tools is to a common crow.
I don't think we have ever seen DNA as the vector of superpowers before - but we have seen random chemicals or energy bursts achieve the same. Who knows what was in that syringe in addition to the DNA strands? (Not Stamets, certainly!)
Even though it took a few episodes, we finally learned that yes, there was plenty of evidence - nicely also matching horrible Klingon torture, which would be by design. It's pretty clear the House of Mo'Kai knew exactly what sort of scrutiny their creation would face when delivered to Starfleet...
Water coming and going was a big part of the early Black Alerts. Apparently, there's a cosmic reservoir somewhere. (And since the network reaches everywhere, and can physically support humanoid life on occasion, the exact specs of "somewhere" need not concern us much.)
So we should be thankful that a time machine was involved.
Why not?
I mean, it was clear all through the adventure that Control wanted the alien probe data, and did all sorts of evil things to get it - meaning it was evil before getting it. Our heroes at one point speculated that it wanted the data in order to become more sentient, which is perfectly possible - there's always room for improvement there. But we don't need to think this was any sort of a time loop where Control only becomes evil by receiving the seeds of evil from a future where Control is evil, or anything. The AI simply was hostile to mankind by original design, and started acting on it at some point (possibly much earlier than his framing of Spock, quite possibly decades earlier).
Why did it frame Spock, then? It had the means of killing people within Starfleet facilities, implicit and explicit, so either it didn't want Spock dead, or was too late in realizing that Spock Must Die! and let him slip beyond its remote assassination means, so it proceeded to make Spock hunted and then killed in that process.
Why would it want Spock dead? To cover its virtual buttocks, most probably: an expert witness on how the future will unfold would do harm to Control's chances of making it to true godhead.
But corollary to all that: why was Control's influence limited to S31 assets? Why did it not hijack NCC-1031, too? And if it could not, why could it hijack Starbase 5 to kill "Spock's victims" and fake the records?
Or did Control send S31 operatives to kill the three (because that's what the operatives do), and then try and do the same with the hero ship but fail because Leland was too busy with other stuff and Georgiou and Tyler did not cooperate? I mean, assassinating Spock at that point would already be too little, too late. But surely agents who could kill at SB5 could be expected to cripple the Discovery or something?
Timo Saloniemi
Ash Tyler's story that he survived Klingon torture for seven months because of L'Rell interest in him...
...Is simply a cover story, as nicely explained by previous posters. Yes, L'Rell and Voq had an affair, but Tyler's body need not have been involved in it in any fashion. But Tyler being in the hands of L'Rell's faction ever since the capture at the Binaries is likely: this House did run a prison ship and was famed for its interrogators and all, and did have Starfleet prisoners other than Lorca and Tyler/Voq, the two that were specific pawns in L'Rell's games.
Whether House of Mo'Kai would keep a random human prisoner alive for six months is unknown. But Klingons do take prisoners, habitually (they just don't take hostages to protect their own skins, because that gets them slain for cowardice), and Tyler might have been the guy unfortunate enough to outlive his 123 compatriots. At least for the most part (that is, with sufficient body parts more or less intact).
Spock's functionality while temporarily insane was... variable. But thinking on it, it seems it simply degraded more and more as more time passed following his mind meld on the Red Angel. Vulcan brains and all, thinking on impossible paradoxes...
I like that one. It's not so much the doing of the meld itself, but of Spock driving himself insane till a powerful telepath slaps him in the frontal lobe like any good Vulcan Healer.
Also, how did Michael Burnham perform the "miracle" of stopping the Kelpian genocide?
Did she? We never learned there would have been a genocide in progress. What happened was that the Ba'ul had been told to cease and desist; they fired a set of red rays to their "pylons"; and lo, the pylons did cease to work.
Burnham Jr. just knew she had to be there so that Saru could see her. She didn't need to actively do anything with that suit, which for all we know did not have the optional extras and accrued goodies of Burnham Sr.'s suit.
The AquaBomb plot
...What's the problem there? SF already had basic intel that Klingons were geologically vulnerable to such bombing, and if they did not, Tyler would have provided some, and if he did not, Emperor Georgiou would have been familiar with the innards of all things Klingon, be it conquered homeworlds or cut-open warriors.
That the plot then could be turned into the blackmail scheme is the harder pill to swallow. But we saw the aftermath and could appreciate that the Klingons craved a leader, any leader, under any pretext. L'Rell just had to posture louder than her competitors - and those competitors clearly saw advantage in letting one fool try first before they would step in and take the reins. After which it was standard Klingon backstabbing politics all the way.
the Giant Space Tardigrade that can magically teleport
Most Trek superbeings can. Some choose to look vaguely humanoid, but few are indicated to actually be that. Probably it's no more curious than the ability to do calculus is to us, or the ability to use tools is to a common crow.
injecting Stamets with Tardigrade DNA so that he too gets magic powers
I don't think we have ever seen DNA as the vector of superpowers before - but we have seen random chemicals or energy bursts achieve the same. Who knows what was in that syringe in addition to the DNA strands? (Not Stamets, certainly!)
Tyler's chainsaw surgery that leaves absolutely no evidence
Even though it took a few episodes, we finally learned that yes, there was plenty of evidence - nicely also matching horrible Klingon torture, which would be by design. It's pretty clear the House of Mo'Kai knew exactly what sort of scrutiny their creation would face when delivered to Starfleet...
The Tardigrade goes into a cryptobiosis state by shedding nearly all the water in its body but then i'ts ejected in SPACE where it gets all its water back, apparently, in an instant!!! Where does that water come from?
Water coming and going was a big part of the early Black Alerts. Apparently, there's a cosmic reservoir somewhere. (And since the network reaches everywhere, and can physically support humanoid life on occasion, the exact specs of "somewhere" need not concern us much.)
The chronology for Season two seems completely out of whack.
So we should be thankful that a time machine was involved.

They say that Control had been modified by a version of it from the future but that future version came with the modified probe ( episode 7 "Light and Shadows"). So who framed Spock for the murder of three people and why? Since it was way before Control was changed then it couldn't be it.
Why not?
I mean, it was clear all through the adventure that Control wanted the alien probe data, and did all sorts of evil things to get it - meaning it was evil before getting it. Our heroes at one point speculated that it wanted the data in order to become more sentient, which is perfectly possible - there's always room for improvement there. But we don't need to think this was any sort of a time loop where Control only becomes evil by receiving the seeds of evil from a future where Control is evil, or anything. The AI simply was hostile to mankind by original design, and started acting on it at some point (possibly much earlier than his framing of Spock, quite possibly decades earlier).
Why did it frame Spock, then? It had the means of killing people within Starfleet facilities, implicit and explicit, so either it didn't want Spock dead, or was too late in realizing that Spock Must Die! and let him slip beyond its remote assassination means, so it proceeded to make Spock hunted and then killed in that process.
Why would it want Spock dead? To cover its virtual buttocks, most probably: an expert witness on how the future will unfold would do harm to Control's chances of making it to true godhead.
But corollary to all that: why was Control's influence limited to S31 assets? Why did it not hijack NCC-1031, too? And if it could not, why could it hijack Starbase 5 to kill "Spock's victims" and fake the records?
Or did Control send S31 operatives to kill the three (because that's what the operatives do), and then try and do the same with the hero ship but fail because Leland was too busy with other stuff and Georgiou and Tyler did not cooperate? I mean, assassinating Spock at that point would already be too little, too late. But surely agents who could kill at SB5 could be expected to cripple the Discovery or something?
Timo Saloniemi