People seem to be a little bit confused as to how certain elements of CIVIL WAR and its tie-in books fit together, which kind of lends itself to a discussion about how time passes in comic books and crossovers in general.
The first thing you've got to keep in mind is that all of the comic books that come out in a given week aren't necessarily happening at the same time. Heck, some stories take six issues to fill in the events of two hours in a character's life, where another story will leap ahead months in the space of a few pages. So time is not a constant across the titles--there's a general overall sense of the passage of time (but even that tends to compress the further away from the present you tend to go, with certain "tentpole" milestones charting the way into the past. Which is to say that today we might reference HOUSE OF M as having happened a year ago, or six months ago, but the further away from right now we get as we move forward in time, the less relative space will have taken place in that interim. It takes a certain elasticity of mind to be able to follow this.)
The second thing you have to keep in mind, especialy when you're dealing with a character like Spider-Man who'll appear in several books every month is that the "break-point" for a character to move between stories and titles isn't necessarily in-between issues. In many cases, it's least likely to happen in-between issues, since we so often leave off a book with a cliffhanger situation that's immediately followed up on in the subsequent issue.
So to put this in practical terms that you can understand, the sequence of events in CIVIL WAR goes like this:
CIVIL WAR #3-4: The heroes battle it out at the chemical plant. Goliath is killed
AMAZING SPIDER-MAN #533-534/FANTASTIC FOUR #538-539: The "Battle of Yancy Street" takes place as prisoners are moved from one location to the next. The Thing decides to leave the battlefield.
FANTASTIC FOUR #540: Reed and Sue have a fight. Sue storms out. Ben says, "She's left you, huh?"
CIVIL WAR #4: Hours or days later, Sue and Johnny leave the Baxter Building with their things, intent on joining up with Cap's crew.
There's actually some more FF-related events that go on in and around some of the events I just listed, but because they'll be happening in books that we haven't released yet, I'm not including them in this example. And the reason we try to do things this way is because we're trying to serve all masters. If you only read FANTASTIC FOUR, we want you to feel like you're witnessing teh story, and not simply getting a cliff notes version of what's happening elsewhere. Same thing with CIVIL WAR proper. Eventually, both of these books (and AMAZING SPIDER-MAN, and everything else) will be collected as individual trade paperbacks or hardcovers, and we'll want those books to read well on their own, even though they all tie in to the larger CIVIL WAR event.
You're welcome.
More later.
Tom B