After some bumbling around trying to work out what went wrong, Neelix inadvertently supplies the missing piece of the puzzle - it's the shuttle that is being ripped off the nacelles, not vice versa. The tritanium alloy of the hull is depolarizing, making the fuselage go faster than the nacelles. Fixing it is simple, and our heroes run a successful simulation. Janeway okays a real flight, despite concerns that we may not be ready for such a massive technological advance. However, she wants to appoint Kim as the pilot - Paris has a slight enzymatic imbalance in his cerebellum which might possibly cause a brain haemorrhage.
Paris does some begging. He says he's never really achieved anything special in his life, and he is desperate for the chance to become the first man to reach Warp 10. Janeway relents, and he sets off on his mission. The shuttle - dubbed the Cochrane after the inventor of Warp drive - reaches Warp 10 and vanishes from Voyagers sensor and communications range.
It re-appears shortly afterwards and an unconscious Paris is brought on board. When he wakes, Tom reports that he was passing through every single point in the universe simultaneously, including Earth and even Voyager itself - truly infinite speed. The shuttles computer contains information on literally thousands of planets - over five billion gigaquads worth in all. However, there are some remaining problems - Paris can't really explain how he navigated the shuttle back to Voyager other than to say that he saw that they were looking for him so he took the engines off line and ended up back where he started. Nevertheless, everybody is delighted.
Unfortunately, Paris begins to undergo medical difficulties. He collapses whilst talking to B'Elanna and is rushed to sickbay. It turns out that his body is mutating - it can no longer process water or oxygen. Despite the EMH's best efforts the mutations get worse and worse and Tom dies shortly afterwards.
Amazingly enough, he soon comes back alive again. His body has grown an extra heart, and all his hair is falling out. While Voyagers resident traitor sends information about the flight off to the Kazon, the EMH continues to work on the mystery. He discovers that Tom's DNA is re-writing itself - three new internal organs have appeared, while some of his normal organs are being absorbed into his body. His personality has also become erratic - even more so than usual - and he is frequently deranged. He seems happy with the changes that are overtaking him, and resents the crew for trying to reverse them.
The doctor comes up with a possible method of curing Paris by bombarding him with antiproton radiation. Unfortunately, he breaks loose during the procedure and leaves the ship in the Cochrane, taking Janeway with him. Voyager gives chase but is soon outpaced by the transwarp shuttle. After three days of searching they find the shuttle landed on a nearby planet. The EMH realizes that Paris has not just been mutating but evolving at an incredible rate. On beaming down to the planet they discover that both he and Janeway have turned into beings that closely resemble giant Newts - and furthermore they have mated and reproduced!
Chakotay stuns the two and returns them to the ship, leaving the offspring behind to fend for themselves. The doctor is able to reverse the process with his antiproton bursts and returns Paris and Janeway to normal. The Captain admits to Paris that she has thought about having children, although she had never really thought about having them with him. Voyager continues on its way with everything back to normal.
Voyagers "Initiations" is a DS9-style dud - there's nothing wrong with it as such, but it's very boring. But it's an exception for this series - Voyager duds are almost always down to the fact that the whole concept of the episode is just plain rubbish. And while elaborate attempts are often made to paper over this with lashings of technobabble, it just doesn't work. I'll go through Threshold in some detail below, but take a quick look at some of the others above. In "The Swarm", Janeway just arbitrarily decides to go through the space of an species of unknown strength, despite warnings that they will not tolerate such a trespass, in order to avoid a few months extra travel on a seventy year journey. This is a massive violation of Starfleet principles - and Janeway has shown on other occasions that she will sacrifice virtually anything in order to uphold her principles.
In "Sacred Ground", the whole thrust of the episode is that it can be a good thing to abandon common sense and act irrationally. This is diametrically opposed to the usual philosophy of Trek, and makes the episode part of the quite disturbing pre-millenial trend towards nonsense like astrology, palmistry, etc.
"Favourite Son" is just plain silly. I always refer to this episode as "Planet of the Bimbo Women".
But now we come to "Threshold". In this episode the USS Voyager constructs a shuttle capable of achieving Warp 10. A single small ship, stranded far from home and low on supplies, over a period of one month, achieves something that has eluded the entire Federation for a hundred years. This alone is fairly absurd, but it only sets the tone for the rest of the episode. On returning, Paris turns into a giant Newt! Trek has been guilty several times of claiming that a change to your DNA will automatically cause your body to alter in order to match, but this is one of the worst offences.
We're then told that Paris has actually evolved into a future form of Humanity. This is even worse - evolution is NOT a pre-determined path which turns one animal into a more "advanced" one. Rather, a random mutation propagates through a species over many generations because it is better suited to the environment. A massive change which happens to one individual within its lifetime is not evolution, and in any case Paris was certainly not becoming better suited to his environment, but rather the reverse since Voyagers atmosphere became poisonous to him.
Having then died and come back to life, he kidnaps Janeway and takes a ride at Warp 10. And with literally all the universe to choose from, he just so happens to drop out of transwarp within a few days travel of Voyager. The odds against this must be literally trillions to one, making it just about the most improbable event in all of Trek history.
In this time Janeway and Paris have transformed into that most advanced of all creatures - the giant Newt. The EMH treats them by blasting them with antimatter - yes, honestly - and hey presto, all is well.
Why Voyager can't use the shuttle to send somebody home and back isn't made completely clear - after all, they can now treat the condition easily enough. It's implied that there is some difficulty in navigation, but Paris seemed to manage it on the first journey.
So, all in all a pretty big stinker. Any redeeming features? Well, Robert Duncan McNeill turns in another excellent performance as Paris and his conversion into the Newt is quite stomach churning. The other cast members are up to their usual standard also, while the FX are as good as always. But none of this excuses the basic absurdity of the entire premise.
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