When the Serenity crew meets Shepherd Book again at his commune on Haven, we see he is now wearing his hair in cornrows instead of balled up at the back of his head as he did during the TV series.

Apparently the crew has been to the commune before, because a little boy runs up to them when they arrive and jumps into Kaylee's arms, both having huge smiles on their faces. A man in a helmet also greets Jayne as if they are old pals. (The boy makes a flashback appearance in The Shepherd's Tale.)

Around the campfire that night, Jayne strums a guitar! Who knew? 

At 47:42 on the DVD, Mal has several maps hanging on the wall of his quarters. One of them appears to be an old-timey map of the western hemisphere of Earth.

Notice that at 47:17 on the DVD, River dreams of waking up just before she really wakes up.

At 49:13 on the DVD, notice that, as the crew eavesdrops on Mal's conversation with Inara, Wash throws a piece of food or something at the screen when Mal tells her that Kaylee misses her instead of admitting he himself does.

At 49:34 on the DVD, one of the computer panels is somewhat visible next to Kaylee on the bridge. The phrases "ILLEGAL ACTION CODES" and "FAULT/STOP ON CONDITION" are printed on it, above lights and switches. The device appears to be a mid-1980s model mainframe computer manufactured by Honeywell.

At 50:37 on the DVD, Inara is kneeling and lighting incense in front of a Buddha statue. Buddha was the Indian spiritual teacher Siddhārtha Gautama whose teachings began the Buddhist religion. Buddhism is prevalent in the Asian countries which would suggest a strong presence in the worlds of the Verse.

During their discussion in the Companion training house, the Operative and Mal use an albatross metaphor in relation to River remaining on Serenity. This alludes to the 1798 poem "The Rime of the Ancient Mariner" by Samuel Taylor Coleridge. The albatross was considered good luck by a ship's crewman, but, in the poem, a mariner kills the albatross, cursing the ship, bringing about the deaths of all on board.

After Mal shoots him, the Operative immediately gets back up and attacks, saying he's not stupid, he's wearing full body armor. Guess it was a good thing Mal didn't shoot him the head instead though!

How did Inara know where to set and light the fake incense so it would explode right next to the Operative at a specific moment? And how did she know it was going to explode right at the moment it did, as evidenced by her remark to him, "And that's not incense"? Does she have some psychic abilities of her own? Or did she have some unseen method of triggering the explosion at a specific moment?

The armor worn by the alliance soldiers is different here than the borrowed Starship Troopers armor seen in episodes of the TV series such as "The Train Job".

Like Serenity, the interior of Inara's (former) shuttle is also a bit redesigned from that seen in the TV series.

To aid in the ship's escape from the Operative's forces at the planet on which the Companion training house resides, Serenity drops a number of cry babies to serve as misdirections of which way she has travelled. The cry babies seen here appear more sophisticated than the one cobbled from a Blue Sun coffee can used in "Serenity".

At 1:01:00 on the DVD, Jayne pours himself a drink into a cup with a devil face on it!

Did River use some kind of psychic ability to entice Jayne into opening the storage room and coming in for her, as a means of escape? Or was it just Jayne's own nature of self-preservation and apishness that made him decide he was going to go in and take her out?

Mal reveals that the term "blackrock" is used to designate a planet that is uninhabitable. Here, we learn that there is at least one habitable world (Miranda) that the Alliance has designated as a blackrock in order to hide activities taking place there.

The Shepherd's Tale reveals that the Alliance ship that was shot down by Shepherd Book here on Haven was an A.V.-Sparrow short-range gunship.

Using an old Hollywood trope, only the character we most care about at the commune when Serenity returns and discovers the slaughter there, Shepherd Book, is still hanging onto life, just long enough for a poignant farewell.

The cannon Book used to shoot down the Alliance ship and which is later mounted on top of Serenity, is a modified Flak 38 anti-aircraft gun, used by German forces in WWII. Visit this link to see photos of a model of the real Flak 38.

Zoe tells Wash to warn Li Shen, the Sanchez Brothers, and others who've sheltered the crew in the past to get out now before the Alliance comes and blows them away. Li Shen and the Sanchez Brothers have not appeared in any previous stories told thus far (though the Firefly board game refers to the space bazaar seen in "The Message" as "Li Shen's Bazaar"). The video feeds at 1:07:43 show that the two have already been hit. The feeds identify Sanchez Ship Repair and Storage on Boros and Li Shen at the K-3 Mining Post on Whitefall. Whitefall was previously visited in "Government Goods", but neither Li Shen nor the K-3 Mining Post was mentioned.

During his speech to the crew on Haven, Mal refers to the Alliance men as "bungers". This may be one of Joss Whedon's fancy English slang terms, but I've been unable to find one that seems to fit its use here. Possibly, "bunger" means "asshole", as in "bunghole".

While passing through the space "shipyard" of the Reavers at 1:12:17 on the DVD, there appears to be another Firefly-class ship in the top left corner of the screen. (Assuming that we are being shown an approximate POV from Serenity; otherwise the Firefly might be interpreted as Serenity herself.)

Jayne's expressions of relief after the ship has passed through the Reaver shipyard at 1:13:40 are amusing.

At 1:13:58 on the DVD, there appears to be a large number of metal boxes stored down in the little-used compartment at the prow of the ship, below the bridge pilot consoles. In the TV series episodes, the compartment appeared to be empty.

The spacesuits worn by Mal and Zoe as they scan the air at their landing spot on Miranda appear to be the same style as the ones used in several episodes of the TV series. Jayne is wearing a different, yellow environment suit not previously seen.

At 1:15:23 on the DVD, on the left-hand side of the screen, a large stairway/ramp is seen. This is based on a design at Robson Square, the civic center of Vancouver, Canada.

The shoes worn by the dead man at 1:16:27 are slightly modified Nike Flightposite III basketball shoes.

At 1:16:36 on the DVD, there appears to be a reflection in the glass wall behind Wash of a member of the production crew kneeling down to stay out of view of the rotating camera!

At 1:16:43 on the DVD, the dead face River sees during the psychic flood that overwhelms her on Miranda is the same one she got a flash of when she was triggered by the Fruity Oaty Bar commercial in "Triggered".

At 1:17:17 on the DVD, the crew finds a small ship crashed into the side of a building. The look of the on-location set is hampered by the fact that there is no skid track leading up to the building! 

Oddly, the ground vehicle Jayne peers into at 1:15:38 on the DVD also has the C57D code on it! Maybe the vehicle and its occupant were also part of the same research and rescue division as the ship, and was overcome by the Pax while investigating the effects on Miranda.

When River plays back the holographic log on the crashed ship, most, if not all, of the images of the dead presented in it are the same ones River has been seeing in her psychic flashes.

The researcher in the holographic log indicates the chemical substance that inadvertently caused the deaths of most of the population of Miranda (and turned the survivors into Reavers) was an experimental compound called G-23 Paxilon Hydrochlorate (Pax). It may be that the G-23 designation is a reference to the modern day G23 category of degenerative basal ganglia disorders of the brain, which can cause, in some cases, a paralysis of the will of the subject, rendering them essentially immobile and uncaring. Additionally, the short-form name Pax is also a term for an enforced peace.

At 1:19:16 on the DVD, River is mouthing the words of the researcher in the log as she says them. 

The position of the label on the blue bottle that Jayne slides across the table to Simon changes a couple times from the slide to Simon picking it up.

Notes from the Audio Commentary by Joss Whedon on the DVD

Joss remarks that scenes of the dead city on Miranda were shot at Diamond Ranch High School in Pomona, California. The crashed research ship is shown as having crashed into the school band's rehearsal room.

Unanswered Questions

Why was the Pax substance released, apparently untested, across an entire planet? Didn't the researchers test it on individuals first, where they would have learned of the effects on a small scale? That's SOP for any scientific establishment. 

Memorable Dialog

much, much worse.wav

hiding ain't a plan?.wav

it's not your way.wav

if anything happens to me.wav

kind of a tease.wav

try not to faint.wav

you can't make me angry.wav

do you want to run this ship?.wav

we'll get off.wav

or we could talk more.wav

that crossed my mind.wav

not very Christian of me.wav

I don't murder children.wav

a lot of fine ways to die.wav

helpin' me out or takin' your leave.wav

I aim to misbehave.wav

can't do something smart.wav