Xenoblade 1 and Xenoblade 2 were taking place concurrently in different dimensions. XC2 takes place in the original world, in which Klaus re-created life after his experiment destroyed it.
Klaus lost half of his body to XC1's world which became Zanza and he died when Shulk killed Zanza. (and that's Shulk's voice you hear as he's killing Zanza)
The 3rd missing Aegis is Alvis from XC1 and was lost in an interdemensional accident (creation of XC1's world)
The Monado exists in both worlds but Malos had the one in this world
The female scientist with Klaus was who became Meyneth in XC1
Unknowns:
Why Pyra/Mythra came back to life and were separate. Maybe the Conduit/Zohar used it's last bit of juice to replicate its existing data on them? Or maybe it was just a final gift from Klaus?
When Gramps "crossed the rift" did they simply just move below the clouds find an ocean did they cross dimensions into Shulk's new world?
Also just the appearance of the conduit/zohar in general. I feel I'd have to go back to Xenogears and refresh myself on The Zohar Modifier/Wave Existence and all that fun stuff.
