gwaah that blows my mind! What i just read. Its neither a new character or Haruhi who caused the time quake. We all know it could be Nagato but it seems Big Mikuru isn't implying that.
Somebody close caused this time quake... Haruhi isn't the cause, can't be Itsuki because people of that time lack the technology to go back in time, can't be Mikuru because causing a time quake could lead to undesirable effects, and that leaves Yuki. Big Mikuru told Kyon that the person that caused the quake was a person close to him, and what person that we havn't yet eliminated could possess the power to cause time quakes?
Another spoiler containing an explanation to the explanation
Spoiler! :
Yuki also listens to whatever Kyon has to say or requests, Kyon at times wishes that he could lead a normal life. Seeing this, Yuki decides to give Kyon the choice of having a ordinary life, with no super powered god girlsrunning amock, or a crazy out of control world that has the constant threat of Haruhi recreating the world.
That's the real story, you've been spoilerised! lol Hence the reason why I said SPOILER
------------Spoilers telling the ending of the climax in volume 4-----------
Spoiler! :
You soon learn how Nagato changed the 3 years currant era to give Kyon a choice, the data thought something thing also gets angry and threatens to delete nagato, however Kyon threatens back by exposing the entire truth to Haruhi. Deleting Kyon too would also produce unwanted results, so Nagato doesn't get deleted.