I have to admit, that while I found this episode exciting and well acted, I found it irritating as well. Admiral Nelson has a distinct blind spot when it comes to anyone he considers "brilliant" or "a genius". He bends over backwards to make excuses for them. This particular specimen is a Naval man, which makes it worse. I can't see the Navy allowing such behavior to go by the board because the man in question is "under a strain".
Captain Adams might be brilliant, but whomever put him in charge of anything needs to have his head examined, because Adams has a sublime disregard for anything but his own interests. He ignored the potential danger of the sonic barrage because to abort the missile launch would cause a delay in his work. He seemed convinced that the explosion would have taken place regardless--but he didn't know that at the time. He shows little real concern for the 20 men who died, or even in seeing that such a tragedy could not occur again. His primary interest was in exonerating himself.
Nelson might think he was under a strain, but I think he was obnoxious. His slighting of Captain Crane was too deliberately done. He did, in fact, outrank Crane--Crane is a Captain only by virtue of being in command of a ship, his Naval rank being Commander--but that does not alter the fact that Crane has the final authority over the ship.
I didn't really understand why Adams was so frantic to collect more information--it seemed reasonably clear that the giant manta was the source of the ultrasonics. After capturing the baby, it became painfully clear that the giant was a source of considerable danger.
At one point, it suddenly occurs to Nelson that the sonics could affect their armament, and snaps off an order to disarm the nuclear warheads. Moments later--before the Missile room crew could have even begun disarming the missiles--Adams provokes the giant manta into attacking them again. This alone should have gotten him tossed into the brig. Nelson did unbend enough to chew the man out.
Not five minutes after promising to be a good boy and never, never endanger the Seaview again, Adams did exactly that. Nelson should have guessed that Adams had something to do with the newest attack, but at least he had sense enough to order the baby manta released. He also made the decision to kill the giant manta (a shame really, because the manta was only protecting itself and its offspring). Adams, of course, sees this as just another maneuver to thwart his pursuit of the truth. He cannot understand that he was probably never considered directly responsible for the missile explosion and the deaths--it was his self-absorbed judgement that was being questioned. And he proves it all over again. Knowing that the Seaview is in dire straits, he locks himself in the laboratory and provokes the manta yet again.
Nelson manages to cobble together a gadget to keep the manta at bay (he's rather good at that, you know) and they manage to break into the lab and take Adams into custody. Having collected sufficient evidence, Adams is stunned when Nelson points out that his actions have rendered the whole situation moot--he's completely blown his career. Adams somehow seems to think that killing the manta will somehow make everything "all right" and breaks away to get outside the sub and tackle the manta alone. For some reason, even though he's already stated that they are going to kill the manta, Nelson brushes off the subject when Adams demands that it be killed. So you could say that Nelson is partially responsible for Adams escaping from the brig.
You would have thought that Adams would get himself killed in the confrontation--that's usually how it goes, but in this case Nelson and Crane managed to haul him back, killing the manta in the process. It never occurred to any of them that if, as they thought, the manta was a natural, previously unknown species, then there are presumably more of them out there to provide hazards for man's technology. They don't even know if the manta they killed was, in fact, responsible for the missile explosion. A strong probability, perhaps, but not a certainty.
You know, it would have been fun to see later episodes with the Seaview travelling the oceans with her foster child trailing along....