How does Malcolm get the idea in the end?

Question

I will try my best at not divulging plot details.

Towards the end of the movie, Malcolm and his crew reach Mr. Universe's abode with the intent of broadcasting the recording made by (planet) Miranda's (late) lab scientist.

Just prior to this, when talking with his crew about the above mission, he deduces that Alliance probably wanted to capture River, and, thereby keep that "incident" secret.

In the first half of the movie, we see River kept having visions of reavers in her dreams only. We are not shown a scene where we can deduce Alliance was responsible for the "incident" prior to the scene where Malcolm and his crew visits planet Miranda.

In the opening scene, the Assassin shows his concern to the Alliance scientist that (the psychic) River was demonstrated in front of senior Alliance members (to show that she was a capable weapon). And because River was psychic, she could have read minds of the senior members and come to learn of "the incident", and thereby Alliance's involvement.

But how does Malcolm finally deduce this?

Answer 1

You're missing key points of the story here. I'm not sure if you've seen Firefly.

• River was enrolled in an Alliance academy (or so her family thought). Important to note here is that the Alliance contacted River's family for what was later revealed to be a sham.
• Simon specifically rescued River from an Alliance facility.
• As long as we've known him, Malcolm has had a strong opinion about how the Alliance seeks to exert control under the guise of bringing peace. Malcolm has firsthand experience here, he was on the not-so-peaceful end of the stick that the Alliance used when invading sovereign planets and territories.
• Jayne once tried to sell out River and Simon. He did so by making a deal with the Alliance.
• Serenity and its crew are being hunted by an Alliance operative. The Alliance's involvement with Serenity clearly focuses on River.

Every step of the way, the Alliance is involved.

Furthermore, consider that Malcolm is negatively biased towards the Alliance. The experiment on Miranda was clearly an attempt at exerting mass control over a population. Malcolm already considers the Alliance to wish to exert control over the population. The experiment fits neatly with the Alliance: its purpose, scale, funding, ... all point to it being Alliance-funded research. Further confirmed by Alliance agents trying to stop Mal and his crew from getting the word out.

To be fair, there is one possibility: what if the bad guys aren't actually Alliance, but they simply hide among Alliance ranks?

While that is a technical possibility, keep in mind that this distinction does not matter to Mal. He already dislikes the Alliance, and if there are conspiracies or black ops operating inside the Alliance government, that just makes things even more clear cut to Mal: The Alliance is a problem that needs to be rectified.