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After watching the Firefly series and the movie Serenity, I'm still trying to figure out how the Alliance was intending to use River Tam as an assassin. Was the Alliance simply trying to create superior assassins for use within their territories? Or,

was she created as a weapon to deal with the Reaver problem created by the Alliance? I feel like there might be a connection between the 2 Alliance experiments of creating assassins and accidentally creating Reavers.

Is there an in universe explanation for the Alliance's intended use of River as an assassin?

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As far as what is stated on-screen by Alliance personnel, there's no direct link between the Reavers and the psy-ops program that River was part of. While it's likely that all Alliance scientific research is connected in the sense that it all falls under the government umbrella, there is no evidence that the Reaver problem led directly or indirectly to the psy-ops program.

The only concrete link between the two of them was the fact that one high-ranking government official, who happened to know the truth about the Reavers, was put into the same room with River while they were busy activating her telepathy. The knowledge embedded itself in her subconscious and is part of what kept her "crazy". This was obviously unintentional, given that the person responsible was punished rather severely.

The best description we get of the program that River was part of, is the opening scene of Serenity. In that scene, the program is described as just another Alliance weapons program. We can surmise that the Alliance had made some kind of medical or scientific discoveries that led them to believe they could create programmed, psychically-active assassins. This is something that governments throughout Earth history have toyed with, with varying degrees of seriousness, under the premise of "no matter how crazy it sounds, it's even crazier to let someone else figure it out first." It is fully in line with the Alliance's behavior to fund such a program as soon as they thought it feasible (it's almost a natural extension of the Operative program.)

The description of what was done to create the Reavers and what was done to create assassins like River are also not very similar. The Reavers were the result of a chemical weapon gone awry, while River was the result of brain surgery. The former was an attempt at mass behavior modification to reduce aggression in an entire population, while the latter was a targeted attempt to activate specific neurological capabilities in a specific set of people.

Other than both experiments being roughly "brain-based" (and both ultimately being a devastating disaster for the Alliance :)) there doesn't appear to be much of a direct link between the two.

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    @Thaddeus the attempt to use the PAX on the population of Miranda was very much intentional and planned, but the effect was supposed to be to calm down the people. The death of the entire planet, except for the 0.1% that became Reavers, was clearly not the goal :) – KutuluMike Sep 20 '12 at 18:30
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    I dunno: in the final showdown on Mr. Universe's planet, when River stays outside the door to deal with the reavers, I got the sense that she's finally doing what she was designed to do; and the whole lead-up before that has a sense of inevitability about it -- not only can River defeat the Reavers, but only River can defeat the Reavers. (Notice the similarity of their names.) – Martha Sep 20 '12 at 23:53
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    @Martha: I disagree. For all that she is brilliant at it, River hates and fears the violence she can unleash, this and horror of the Reavers haunts her. At the end of the movie she does for Simon what she could not do for herself, she embraces the violence, it's the only chance Simon has. She chooses to do it because Simon - literally - threw away his old life and put his own wants and needs to the background to care for and protect River. Ergo, River faces her fears (and kicks ass) to save Simon. – Binary Worrier Sep 21 '12 at 6:56
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    (cont) Also, wouldn't a well armed fleet nuking the Reaver ships in space been more effective than one or two highly trained assisans? The assassin program was for covert ops, taking out rival leaders etc, not an anti-Reaver measure. Also Reavers didn't penetrate as far as Alliance space, and it didn't hurt to have a big scary boogy man out there. You can see the meeting now "They kill hundreds every year", "Yes, they kill hundreds of rebels every year, when they start killing thousands they'll come and beg for our protection" I just made all that up, no "canon" in there at all :) – Binary Worrier Sep 21 '12 at 7:03
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    @AidanO well, the Alliance probably didn't consider it a weapon as such, but it was a chemical intended to be unleashed, against their will, on an entire population of people with the intention of changing their behavior and eliminating threats to the Alliance rule of the planet, so I was abbreviating :) – KutuluMike Sep 21 '12 at 15:29
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I thought it was rather clear what they were trying to do - River was one of several children who were identified as having potential psychic abilities. They were experimented on to enhance and develop those abilities.

Their apparent purpose was to create a number of telepathic spies and/or secret agents. These people could be used in any number of ways, ranging from internal security to infiltration and even assassination. A telepath would excel at any of those - they could detect anyone in your organization who was planted as a spy (or who had developed disloyalty), could easily infiltrate any organization (it's easy to get hired if you know exactly what the interviewer wants to hear), and assassination would be simple for someone who knows exactly how to get through your security and how to become your best friend.

The changes done to River's mind (stripping the amygdala, among other things) were part of this experimentation process. In the series, we learned that this process had stripped away her ability to push aside her emotions.

This is obviously not a desirable trait in a psychic spy, so presumably the Alliance thought they could reverse the damage once they'd enhanced her abilities. That was my initial thought, at least, until I saw Serenity.

When River is exposed to the commercial that triggers her, she seems to go almost completely emotionless. Perhaps the Alliance found a way to actually suppress her emotions - if she couldn't feel any emotion they didn't let her feel, she would have become the perfect agent. She would have been completely loyal, utterly merciless, and without regard for her own safety.

River wasn't turned into an assassin, she was simply turned into the best Operative+ they could make, and her psychic abilities were enhanced. The fact that this made her a brilliant potential assassin and an unstoppable hand-to-hand combatant was merely icing on the cake.

As for being a perfect weapon against Reavers, I strongly doubt that was the Alliance's intentions. To the Alliance as a whole, the Reavers were almost certainly considered a manageable threat.

Consider the Reaver's tactics: They travel in small groups (usually single ships closer in size to Serenity than to Alliance Cruisers). They raid planets and moons, using shock tactics and fury. They charge directly into hand-to-hand combat, eschewing most projectile weapons. They have a certain amount of cunning, but lack any overall strategic guidance or overt command structure. They did, absolutely have larger ships in their fleet, but it's notable that we never see any sign of this until people move towards Miranda.

It's probable that the Alliance thought they could handle the Reaver threat quite easily with their fleet and existing ground forces, so I doubt they would send such valuable assets as River against them intentionally.

A disciplined, prepared military would rip them to shreds.

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There was not a specific goal for them. The Alliance collected exceptional children under the guise of a special academy and experimented on them.

We are not shown whether all of the experiments were the same as River's. However the Alliance has shown that they believe that 'they can make people better' (Mal - Serenity), and this keeps going wrong. Either they create the Reavers (and frantically deny the existence, wipe out the evidence whilst trying to figure out how to stop them) and unleash true horror or they try to create a perfect weapon who's brain implodes and then turns on them.

The most likely scenario is that they were using her as trail blazing research to create a new type of weapon and they would find uses for her once she was up and running; they probably had dozens of ideas for potential uses. A pure assassin role is unlikely as once her picture got out her efficiency would be greatly reduced. Some kind of covert operations would seem likely, she would make an awesome bodyguard, etc.

However, this calls up the question of why they cannot simply ask for a volunteer out of their own elite forces and 'upgrade' them?
The most likely reason is the Alliance arrogance (which is also their downfall) - they feel that they can make people better than people can make themselves whether the people want them to or not and time and time again this backfires with terrible consequences.

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There is a callback in this to Dr. Josef Mengele and the horrific experiments done during the Nazi era on political prisoners and "lesser races". Also we should not forget this is a science fiction trope, as seen in Ender's Game and its sequels. There was a movie in the late 1970s too, about children who were encouraged to play video games (a new thing at the time) which turned out to be a very real battle with alien invaders.

That the experiment was not successful, because River became insane before she became psychic or a weapon, is to be expected. It is bad science to blindly set a goal and then ignore all the evidence that your goal is not being met. The Operative was right about Dr. Mathias' sin, he was too proud. His sin was hubris.

And it is also possible that the entire, expensive, program was working well under the radar of the larger government. Keep in mind that River was sent to this boarding school by her wealthy and well-connected parents. They may even have paid for her to attend. While Simon and his father have a tense adult relationship, the Tams seem to have been indulgent parents to their young children.

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