During the first Tri movie, it's mentioned that it had been a year since the close of the digital gate, and that it had not opened since. If anyone remembers during Adventure 02, the premise was that the loss of the Destiny stones caused the digital world to merge, but BlackWarGreymon sealed the gate.
It's at this point that time becomes alternate for Digimon Tri. Rather than the dark spires reappearing, Himekawa is trying to get her digipartner back, much the same way that Oikawa had lost his partner. She sent Ken, Youli, Davis, and Cody back to the digital world, but they lost to Alphamon. As in dead, both they and their digital partners.
This is why Himekawa is aware that these kids are 'offline' as shown in the computer screen. She purposefully infected Meicoomon with the dark power that Ken as the Digital Emperor had used in the form of control bands. The assumption is that she figured if she corrupted the digital world, it would force a reset to create homeostasis between the digital and real world. But she also has to deal with the original DigiDestined.
The other possibility is that Himekawa intended to get her partner back by recreating a digital partner, but instead got Meicoomon who wasn't a perfect digital creation, hence the infection, figured out that she would have to force a reboot and began eliminating the DigiDestined, starting with Ken, Davis, Youli, and Cody, and it was in fact Meicoomon who killed the kids.