Having been briefed on the importance of her mission by Mr. Bond, Miss Murray sets out for Cairo to retrieve burned-out former adventurer Allan Quatermain from an opium den. Then, in Captain Nemo's Nautilus, they head for Paris, there to rondevous with a certain Inspector Dupin. They are apparently there to find some missing English doctor named Henry, but they get a bit more than they bargained for when instead they encounter his associate Edward.

After turning Edward Hyde/Henry Jekyll over to the government, Murray, Quatermain, and Nemo set about their next task: infiltrating an Edmonton girl's school, which has been the site of several "miraculous" visitations by an unseen being. The trio encounter and detain this being, which turns out to be an invisible man named Hawley Griffin. Afterwards, Mr. Bond explains their true mission: to recover the government's only sample of Cavorite -- an anti-gravity element -- from a villainous Chinese crimelord known as the Doctor.

Miss Murray, Griffin, Quatermain, and Jekyll set off through the Limehouse district of London to gather information.  Based on what they find, Murray concludes that the Doctor is constructing a deadly airship within the abandoned Rotherhithe tunnel, and using a poorhouse to conceal it.  Murray, Quatermain, and Griffin infiltrate the Doctor's underwater lair in order to confirm their suspicions.

While Hyde provides ample distraction, Quatermain manages to take possesion of the Cavorite without being noticed.  Cornered by the Doctor's guards, Murray, Quatermain, Hyde and Griffin make a daring escape into the Thames river, where they are retrieved by the Nautilus. Later, Mr. Bond shows up to congratulate the League on a job well done. He then delivers the Cavorite to his mysterious superior, "M", whose identity we finally learn.

5: "Some Deep, Organizing Power..." [sample page]

Moriarty reminisces with Bond, while Griffin spies on them, unseen, before meandering back to the Nautilus' dock to relate what he's heard to his colleagues. From Griffin's story, Nemo deduces that Professor Moriarty survived his confrontation with Sherlock Holmes at Reichenbach Falls and now plans to use the Cavorite to bomb London's East End and destroy his rival, the Doctor.  Realizing that they had been manipulated from the beginning, the League now hasten to make up for their mistake by stopping Moriarty.

Hovering over the city in his terrifying airship, Moriarty commences his bombardment of East London.  The Doctor, in turn, counters with cannons and armed kite-borne warriors.  In the confusion, Murray, Quatermain, Nemo, Griffin, and Jekyll are able to board Moriarty's ship by means of a hot air balloon, and confront Moriarty.

Then, just when it seems that the horrors facing London are at an end, mysterious lights are sighted in the sky...