The plot summary for "Confession" has be released. (Credit to With the Will forums!)
time that will come, virus, the return of the homeostasis...
hmmmmm homeostasis(which is what took her over the first time) doesn't really have much lore in most of the digimon franchise, especially in its debut.
but there is more lore on it in xros wars manga. in that manga it was a system made to replace yggdrasil as host computer of the digital world & as the digital worlds god. it also kicked lord bagra out of the kernel(core of the digiworld) after bagra questioned it on the world justice. later on it made a prophecy that a red & black dragon would destroy the digital world. that red & black dragon turned out to be zeedmillenniummon.
that manga really isn't canon to the anime universe as far as i can tell, but it dose bring up a theory on whats up.
“The time… draws near…”
millenniummon is a being of time. theres always been an off chance millenniummon secured a way to revive should ryo have defeated him.
now where did the dark spore that turned ken into the digimon emperor the first time come from? millenniummon. its quite literally a piece of millenniummon.
then theres the virus. when meicoomon went all zerker on leomon an X appeared on meiko's digivice
the dna X could mean X-Program. the X-program is a virus thats always created by yggdrasil to clear out the majority of digimon after the digital world reached maximum capacity outside of a chosen few.
so then, what would happen if the ENIAC went berserk? or got infected by a virus from an outside source? like say
misses smiley?
the whole thing about gennai going to them for help has been a good bit off since the get go.in 02 he clearly stated that he was purging information on the digital world from government databases because he knew they couldn't be trusted. so why would he suddenly go to a government facility for help before izzy? why would he not inform izzy of this development?
the princess river sushi is clearly a poisoned dish.
so what if ENIAC got tampered with & created an X-program which made it so those infected would go on a digimon killing spree with the survivors being infected by it? but so far it dose not seem to affect humans. so then, what could cause ken to go digimon emperor? the virus. unlike anyone else, ken has a piece of a digimon in his neck

if it can be copied via bar-code scanner theres not much stopping it from getting infected & in turn empowered.
this time it may not even be ken or the digimon emperor in control but rather millenniummon.
there's also something else to consider. it was remarked earlier how the dna X looks like apocalymon's arms.
apocalymon is millenniummon's & millenniummon's two former halves: kimeramon and machinedramon's variable move in anode/cathode(which turns a digimon into another digimon)
makes you wonder if a renewed millenniummon is gonna spring forth from ken's neck or back....