(The image above is © copyright 2003 Marvel Characters, Inc. The text here, except where otherwise credited, is © copyright 2003 Jess Nevins, and may not be duplicated, in part or in whole, without my permission).

Page 1. "I am observing events...I must not interfere...I merely watch."
The person speaking is the 1602 version of The Watcher. In the Marvel Universe The Watcher, an all-powerful alien, lives on the moon (seen in Panel 1) and observes events on Earth; he is one of a race of aliens who observe but never interfere due to a tragic event in their past.

Janssen Choy says, "the diction and vocabulary of the Watcher on the first page is modern, and might represent whomever caused the events of 1602, since he's obviously not from the time period of 1602."

Page 2. Panel 3. Kelvin Green notes that Peter's "I can't climb" is ironic considering the abilities of his Marvel Universe counterpart.

Page 3. Panel 3. "Through fire and water, earth and air...."
This is undoubtedly a phrase of significant mystical provenance. Interestingly, though, a quick Googling shows that it's used in the "Invocation Employed Towards the Conjuration of Compassion" from Anton LaVey's Satanic Bible.

Page 4. Panel 2. Don MacPherson says, "On Page 2: Peter can't climb, so Rohjaz fills in as Spider-Man in a manner. And on Page 3, he throws a net on the monster-form of Virginia. Given the Marvel elements, one can't help but be put in mind of Spider-Man's webbing when considering the net.  Twice, Rohjaz fills in for the "missing" Spider-Man."

Page 5. Panel 2. Most of the runes in the circle around Virginia Dare are Futhark, a.k.a. Norse runes. There's a good chart of them on the Web of Futhark.

Janssen Choy says (echoed by Kelvin Green), "The candles around Virginia are the red and black candle that Strange mentions in his vision.  With them and the net accounted for, that pretty much kills the red herring that the items are somehow related to the origin of Spiderman."

Pages 6-7. Janssen Choy says, "The monk that attacks Magneto might be the historical analogue of Tomas Torquemada, the head of the Spanish Inquisition in the non-divergent normal history before 1602. His relationship with the Pope, and the Spanish craftsmanship of the knife would suggest as much."

Page 8. Panels 3-6. This would seem to resolve the debate as to the identity of the Grand Inquisitor. He is the 1602 analogue of Magneto, who in the Marvel Universe is a metal-controlling mutant and the Malcolm X of the mutant world (as opposed to Professor Charles Xavier, who is the Martin Luther King, Jr. of the mutant world).

Page 10. Panel 1. "No. I can push myself off the ground, with my mind.”
In the Marvel Universe Jean Grey is a telekinetic.

Panel 4. "Back when I...when I was a boy."
Just in case this needs to be spelled out for you: "John Grey" is a girl. She's covering up for herself here.

It's possible that the silverish figure on the left is a reference to the silver skinned Silver Surfer, who in the Marvel Universe is a superpowered alien who formerly helped the world-devouring Galactus consume worlds. I don't know who the other three figures are references to, if indeed they are references.

William Stiteler was the first of many (including Adam Frey, Janssen Choy, and Ben Ebert) to point out that the silver figure is likely Colossus, the fire-breathing character may be Pryo or Sunfire, and the man with the haircut Wolverine. In the Marvel Universe Colossus is a Russian mutant who can change into an organic silver metal body, Pyro and Sunfire are fire-wielding mutant (the latter from Japan, and Wolverine--well, you've heard of Wolverine, surely.

Page 11. Panels 1-4. Janssen Choy says (echoed by Paolo Cruz), "The encounter between Jean, Angel, and Cyclops is reminiscent of the love triangle that existed between them in the very early days of X-Men comics."

Page 12. Panel 1. "The Tyrol" is a state in Western Austria.

Page 13. Panels 2-3. “So they looks at themselves as they steps onto land. And they knew that their lives had been saved. Then each of the four of them puts out a hand, And they touched, and gave thanks, standing there on the sand. For the fortune that faovours the brave, the brave, For fortune still favours the--”
Obviously this is a further part of the "Ballad of the Fantastick" mentioned in 1602 #1-2. It also hints at what happened to the 1602 versions of the Fantastic Four. In the Marvel Universe the FF meant to go to the moon before the Communists did; they failed due to improper radiation shielding in their rocket. (That, or the four were struck by Mopee). Perhaps the 1602 version of the FF succeeded where the Marvel Universe FF failed and got to the new world first--that is, America?

Parke Matru points out that the joining of the hands is an important scene in the origin story of the Fantastic Four.

Panel 5. "She's the most dangerous woman in Europe."
The Marvel Universe Black Widow is a skilled combatant and martial artist.

Page 15. Panel 5. "We live in a time of miracles and wonders."
This may be a reference to the Book of Acts, 2:22: "Ye men of Israel, hear these words; Jesus of Nazareth, a man approved by God among you by miracles and wonders and signs...." Mark Schryver wonders if it is "also another tip of the hat to "Miracles & Marvels," Gaiman's legal fund, which Marvel is helping to finance with profits from 1602."

Page 16. Panel 2. The mechanical man puts me in mind of "The Turk" the supposedly robotic chess playing machine of the late 18th century. "Iron Maiden" says (echoed by Doug Atkinson, Kelvin Green, and ArizonaTeach), "This is reminiscent one of the young von Doom's method of swindling the lesser nobles of Latveria.  In the Doom origin in FF Annual #2, he sells a fiddle that plays by itself but ceases to work once Victor has left with the power source. Of course, the device in 1602 proves to be lethal. The use of the mechanical man could  also a reference to Doom's master of robotics."

Panel 3. Michael Denton says, "with Peter's continued frustration at metamorphosising into his MU counterpart, he is assigned to listen to Strange's interaction with Dare, thus becoming a metaphorical "fly on the wall."  Obviously, flies eat spiders and, IMO, this is another "insult" to Peter, a demotion if you will,  particularly when in this issue he seems to have missed out on THE spider that should have made him Spider-man (Strange mentioning that particular spider having some type of strange radiation or aura, IIRC)."

Panel 7. "That fish, for example, when dried and ground, causes a man to become insensible and to feel no pain. A great boon to any physician."
It is true that very purified blowfish toxin--and that's what the fish in question is--when used properly can be an anesthetic.

Page 17. Panel 3. The Watcher, mentioned in the notes to Page 1, can be seen (or, at least, his bald head and cape can be seen) in the lower right-hand corner of this panel.

Page 18. Panels 1-2. As in issue #1, Peter Parquah here is stopped from being bitten by a spider, and perhaps gaining the spider-like abilities which in the Marvel Universe make Peter Parker become Spider-Man. "Iron Maiden" notes that "in addition to the spider, Peter is seen looking at a couple of scorpions with Nicholas Fury.  An foe of Fury's during the Steranko run on Agent of SHIELD, was Scorpio.   He of course was later revealed to be Jake Fury." 

Panel 6. Eduardo Blake says, "Fury's choice of words "...you can take the ley to this cell from my corpse, and vanish into the night" could be a hint confirmint the first assasin identity as the Vanisher."

Page 20. Panel 8. “White deer...white horse, also. White lion-cat.”
In the Marvel Universe there is a white-haired woman with shapechanging abilities who can turn into a variety of animals. Her name is Snowbird, and she is a member of the Canadian super-team Alpha Flight. Many people (many people) have guessed that Virginia Dare is Snowbird. However, Snowbird was invented after 1969, which is the cut-off date for characters' creations. Or so Neil Gaiman said (albeit in not quite so many words). Possibly Gaiman was being coy with us in the interview when he brought up 1969 as the cut-off date. Possibly he was misleading us for the sake of the story. Or possibly Virigina Dare isn't Snowbird, although this panel certainly lends that interpretation weight.

Vince Moore says,

I'm starting to see some strong Norse Mythological parellels here:

I think Virginia Dare is not Snow Bird but Fenrir.  In Norse Mythology, when Fenrir - a wolf, the offspring of Loki - began to grow to large, they felt they needed to bind it.  The God Tyr (patron god of justice) was the only god it trusted.  Tyr bound Fenrir, but lost his arm in the process.  Virginia Dare has not turned into a wolf yet, but I assume that she could and based on the size of the Grifin-like creature she turned into, it would most likely be large.  So if Virginia Dare is Fenrir, that would make Captain America/Rojhas Tyr (and Cap is arguably the closest thing to a god of justice in the Marvel Universe).  Loki has the ability to change into animals in the Marvel universe so he may have possibly passed this ability on to an offspring.

Also, note that during the fight with the assassin that Nick Fury blocks what appears to be a fairly strong sword stroke with a bare arm.  This seems quite suspicious. In the regular Marvel Universe, Nick fury lost his left eye sometime between his Howling Commando days and his CIA/S.H.I.E.L.D. days.  In other words, when he went from being a soldier to a gatherer of intelligence.  I see a parallel here with Odin, who gave up an eye for wisdom and is seen as both a god of war and of wisdom.  Both Fury and Odin are missing a left eye.

The horn that the music box/machine is blowing could be Hiemdall's horn Giallar.  The effect of blowing it should be either to warn the gods or to signal Ragnarok (which Marvel's already been through once, albeit not before '69).  Ragnarok is supposed to be preceded by three unusually long winters and winter appears to be coming.  So it may simply be an assassination device.  Other horns from Silver Age Marvel include the Horn of Proteus which Namor (or others) can use to summon Giganto from the depths of the ocean and the Overkill Horn, developed by Hydra, whose vibrations can destroy entire cities.  Both of these are even more unlikely candidates.

Other possible Norse Mythological Parallels:

Otto Von Doom--Alberich (King of a race of dwarves who were very good at forging magical items)

Magneto--Holler (God of death and destruction; drags victims to dungeon where he tortures and kills them)

Peter Parquah--Balder (God of light, joy, purity and innocence)

Old Man--Hiemdall (Watchman of the gods; can see and hear for great distances)

Matt Murdock--Hod (Blind god who is tricked into killing his brother Balder)

Jean Grey--Alfhild (Maiden who dressed as a warrior to avoid being given in marriage)

Page 22. Panel 4. Queen Elizabeth died in real life on 24 March 1603 of "blood poisoning."

Thanks to: Alicia, Mark Schryver, Chad Underkoffler, William Stiteler, "Iron Maiden," Adam Frey, Eric Limarenko, Doug Atkinson, Janssen Choy, Ben Ebert, Vince Moore, Michael Denton, Parke Matru, Paolo Cruz, Kelvin Green, ArizonaTeach, Josh Orloski, Andrew Donkin, Eduardo Blake, Jeremy Henderson, Don MacPherson, Qapla5.