They don't give these guys much time to breathe around here. Crane and the President no more than arrive at the underwater base when the communications short out, and a strange radio transmission sets the nuclear reactor haywire.
The saboteurs overlook a special marine communications cable, but of course Nelson thinks of it immediately, and heads off to tap into it. (This gives Allen the chance to slip in some lovely undersea footage from the original movie.)
Having reestablished communications, and assumed that the problems are due to sabotage, General Hobson wants to launch an immediate attack against...well, we don't know who. Hobson seems to take it for granted that they all know who the enemy must be, but no names are ever mentioned. The President, very sensibly, refuses to take anything for granted, and will not call a strike until he knows exactly what's going on. Nelson prepares to go off in search of the beam that's causing the problems. Oddly, there is no suggestion of the Seaview (or any other local sub) attempting to evacuate the base. It would have been nice if they'd put in a line or two explaining this omission. Even if the power failure to the reactor had somehow locked up the access hatch, someone could have at least tried forcing their way in while the beam was being tracked.
The powerful team of Nelson and Crane having been split up for the duration, the scenes shift back and forth between the two. Crane makes a vain attempt to shut down the reactor manually, but they do find conclusive evidence that one of the saboteurs is right there at the base, as the man made no attempt to hide the damage he did to the reactor panel. The President decides to begin taking steps, starting with putting Five-Star General Hobson back on active duty.
It was a fairly good bet that Lloyd Bochner would turn out to be a bad guy, but up to this point he could have simply been a concerned, rather too aggressive old soldier. (Like "Trigger-Happy" Tobin from the first season.) After being reinstated, Hobson's motives start to become clear. He states again that they should strike against the enemy--again without specifying who it is. (Nelson could have pointed out the possibility of Enemy Country "A" making it look as though Enemy Country "B" had caused the sabotage, leaving "A" to pick up the pieces afterwards.) Hobson also makes it sound as though he knows for a fact that the President and the others are going to die.
Nelson pinpoints the source of the beam--but does not tell Hobson. He tells Chip that there is no point in telling Hobson until they are absolutely sure, but it seems rather obvious that Nelson already suspects Hobson. Hobson, meanwhile, is sent back to Washington to reactivate his staff. Upon learning that Nelson is coming ashore to track the beam, Hobson blandly informs Nelson that his people have also pinpointed the beam, and that he will meet Nelson and his team--frustrating Nelson no end.
Hobson wants to attack the source of the beam openly, while Nelson prefers a more stealthy approach. He manages to talk Hobson into staying behind as a liason--and promptly listens in as Hobson informs his fellow saboteurs what is going on. Nelson sends Sharkey back to deal with Hobson, but Sharkey makes the classic mistake of standing too close and talking too much, and is quickly put down and out.
Nelson also makes the mistake of underestimating the ice-cold Dr. Lydia Parrish. I would have liked a little more give-and-take at this point. When Nelson says that the men at the undersea base don't deserve to die, she hisses, "One of them does," but there is no discussion of the other innocent bystanders. (Nelson could have mentioned that the one who "deserved" to die was the saboteur!)
Meanwhile, back at the base...Crane has all the main people gathered together and tells them that the reactor is going to blow sooner than expected. It's really hard to say if Crane was telling the truth about that or not. Either way, it served nicely to flush out the saboteur, who was promptly dragged away. (If it came down to it, at least they wouldn't have to die in the presence of a traitor.)
Having lost track of Nelson--but not of the gadget monitoring his heartbeat--Chip Morton goes ashore in search of him. Alone. That was a pretty foolish thing to do. Aside from anything else, they wasted a perfectly good opportunity to gun down yet another nameless member of the crew. They did, in fact, have a sacrificial lamb on hand, who was a seaman--just not from the Seaview. That was a rather nasty little bit--when Chip heard the bad guy's gun fire, he simply ducked down without saying or doing anything--leaving that poor kid to be gunned down. (That was quite a shot, considering that just a few moments earlier the gunman shot at Chip from virtually point-blank range--and missed!)
I did love Chip's reaction when his heartbeat gadget suddenly when off--indicating that Nelson had died. His face twists briefly in anguish, but he has a job to do and he grimly continues with it--although, as it turns out, he could have stayed back on the Seaview. Nelson, of course, has gained the upper hand--his heartbeat gadget was booby-trapped, going off when Lydia attempted to dismantle it. (I'm mean-spirited enough to wish that the self-righteous Dr. Parrish had hit the wall a little harder than she did.) With only moments to spare (natch!) Nelson opts for the direct approach and heaves a crowbar or some such into the beam panel, shutting it off very effectively. Nelson and Co. find Hobson back at the hotel room they had taken for their base of operations. In spite of the fact that Hobson had smashed up their main radio, Nelson had somehow gotten back in touch with the President, who ordered Nelson to arrest Hobson. Of course, maybe Nelson was just exceeding his authority a little bit--if he had, I'm sure the President would forgive him. Given the way Hobson was arguing into the telephone when Nelson returned to the hotel room, it's quite possible that Hobson would not have found his takeover plans so easily accomplished as he had thought. Hobson ended up surrendering without a struggle--which was probably a big disappointment for Chief Sharkey.