And then a completely new city was built right after that event so again, as Mark stated, nothing of consequence ever sticks.
True they got a new "better" city right away, however, if you look at the current plot and situation such a change was needed in order for the current events to take place. The entire reason
that Ixis Naugus is king right now is because
the city was rebuilt from nanites and was run by Nicole. After the Iron Queen took over the city using her magic the public no longer trusts their safety with Nicole and want her shut down. Since Naugus's powers can destroy nanites the publice feels he can protect them and, after destorying Titian Metal Sonic, they have good reason too.
That all seems pretty consequential. True, Nicole could save the day in a future issue and everyone would love her again and forget the whole Iron Dominion mishap but I sorta doubt that's going to happen anytime soon (and if it does it'll likely result in Nicole sacrificing herself). Also there's now the whole Ixis Naugus factor to throw in. Even if Nicole is forgiven the damage is still done: Naugus is still king and it's likely going to take the "secret" freedom fighters to put an end to his rule.
In response to bwrosas and the theorie's around the stolen blue Emerald I think perhaps Eggman Nega took it. Go back to SU 21 Treasure Team Tango. At the very begining we see Nega is running from the zone cops. Also, he stole a Sol Emerald but looses it
. Now go to SU #32 Scourge: Lock-down and read the last page. Zonic states that "Nega has us spread thin." So, Nega is out there, somewhere. Now doesn't it seem likely that if he stole a Sol Emerald a Chaos Emerald might be just as appealing? Also there's the "Egg Jet" Snively steals in SU 37 Scrambled. Snively doesn't recognize it. Could it be it wasn't always there? Also he left the tracker on after swiping it. Why would he do that? It doesn't fit the plan he spilled out near the beginning of the issue, Even Eggman finds it odd and mentions is at the end. Could it be someone was hiding inside it and fled because they were discovered?
Also the fact that Snively spilled out his plan sorta gets me to think he didn't likely steal the Emerald. If he did he would've mentioned it right? Lien-da seems a more likely candidate but where would she hide it? Her quarters are located on the ship, there'd be no logical place to stash it.
There is one other high possibliy I see and that's Shadow, Rouge and Omega or Nack and his posse. After failing to get the Sol Emerald in Treasure Team Tango both teams seemed pretty down. So prehaps they picked themselves up and stole a Chaos Emerald for good measure. I think Rouge's team is the most likely since Omega is on the cover of issue 38. Honestly, why else would he suddenly be there? I guess he'd like his chance to take out Metal and Mecha Sally but really, to find them so soon?