Actually, Axis is perfect where he is. It's fine that he's in a political situation right now, because since this is an origins story, we can explore how he became the villain he usually is.
Also, Alpha Squad still exists, so there is no need to teleport them. The reason they stuck around for several hundred years was the simple fact that they were in stasis on the Skylark for about that long while it traveled.
The events of RtC were made possible by the invention of the FTL drive some time after the events of Spiral Knights. Before then, travel was a good deal slower and required that the crews be put in stasis during the journey.
Is Seatus supposed to timewarp alpha squad in then? Also I'm sort of stuck on where Axis should be going from here, I want him more involved with the fights, but he was more introduced in a political manner.