Roots: Conan Doyle's Sherlock Holmes story The Adventure of the Final Problem. The Dr mentions Frankenstein's monster and asks "Do I look like Tommy Cooper?" (not yet you don't, sunshine...), Lucie likens the gene splicing operation to Jurassic Park and Straxus' cell to the London Dungeons.
Intertextuality: The Doctor's comment regarding battling Morbius - "other times, other faces" may be a reference to not only his Fourth incarnation's meeting of the criminal renegade, but also his next incarnation in Terrance Dicks' BBC Book Warmonger. Alternatively it may be a comment on the controversial 'other faces' seen in the Fourth Doctor's and Morbius' mind wrestling battle in The Brain of Morbius.
Technobabble: Morbius challenges Gallifrey over a 'hyperlink audio transmission' from Karn.
Fluffs: Katarina Olssen mispronounces Solon as "Sollen", prompting Sheridan Smith to follow suit.
Dialogue Disasters: Lucie's constant 'comic' mispronouncing of TARDIS technology. Tss, you guys!
"Zarodnix has a Morbius fixation!"
Dialogue Triumphs: "If you do see another Lucie Miller, give yourself a wide berth" "Why?" "Well, that's the advice I normally give people about you."
Double Entendres: "Give me that wretch from the dungeon, I need him."
Technobabble: Zarodnix's Genetrotron.
Continuity: The Sisterhood were driven from Karn by its new owner, Zarodnix, who shelled them from orbit. At their departure they warned the Time Lords, who immediately quarantined Gallifrey and recalled all TARDISes, then used the times coop to track down any Time Lords who didn't respond. Orthena says that Zarodnix's time particle monitors were able to follow the movements of the time scoop, which is how his agents found and captured the Doctor. Among the artefacts he's obtained over the years include Morbius' Presidential robes, the technology he developed with his own hands and, not least, the very cells from his mind. The full extent of the Sisterhood's psychic influence and telepathic awareness is unknown. Their dispersal chamber takes around forty seconds to do its work. It is a very old model, stolen from the Time Lords.
The Doctor describes Morbius as "a dead Time Lord dictator", and recognises him from his robes; but it appears that Morbius was in his own way a genius, hinting that he fashioned his own stellar manipulator in the style of the Hand of Omega. His title is Lord Emperor, and his citadel, built from the ruins of a thousand worlds (and including the Statue of Liberty from Earth), sits over the very abyss his retrieved brain was driven into millennia ago by the Sisterhood. His phantom reign lasts ten years and sees the removal of Gallifrey's access to time travel, and the fall of entire star systems before it is overwritten by the Time Lords, reviving Karn to pre-Zarodnix time (returning the Sisterhood to the world) and restoring Straxus to full health. The Doctor, presumably because of his closeness to Morbius' fall, is not brought back to life, and all [time travellers?] involved remember the events, Lucie among them. Morbius' stellar manipulator resembles a medallion. It is unable to totally destroy the Eye of Harmony, but can control it or hold its powers at bay.
Earth is said here to be the birthplace of the human race; Zarodnix himself is human. MOrbius' company of slaves includes a million Earth humans.
The Doctor knows Bulek of old [the implication being from the Doctor's time on Gallifrey, possibly as a tutor?] and says he was somewhat doddery even when he was his age. Bulek tells Lucie "Deep isolation is not something to be discussed with those who are not of our world." Gene splicing is an imperfect science on Gallifrey. In the Capitol are several TARDIS holding bays for use in the event of mass time scooping. The Doctor uses the TARDIS' telepathic circuits to contact the Sisterhood, and can feel their minds through them.
Lucie suggests that the idea of her birthplace being a Blackpool service station would not be "that far off" (although she may be exaggerating.) The Headhunter arrives at her house at midnight.
Untelevised Adventures: The Doctor was with Lord Wellington on the eve of the Battle of Waterloo (considering he also gave Napoleon some advice this would have made him a busty man), with the military leader telling him he "always like[d] to have something in [his] pocket for later."
Links: The Doctor quotes himself (the "chop suey" line) from the events of The Brain of Morbius. Straxus' ravaged features as described would appear to resemble that of the decaying Master (The Deadly Assassin)
The Bottom Line: That's quite some fall. There are elements of the story that make for an underwhelming whole - if the first part had rather too much Lucie and not enough Doctor, this part has rather too little Morbius, and the conclusion that all of his conquest is later erased from the timeline only cheats the listener further. McGann gives it his all though, and it's fun to have Nickolas Grace back. But on the whole - a decidedly flat end to a season with such a strong start.