Spend the whole 1st season and maybe some of the 2nd working on building the relationship between the Maquis and Starfleet.
Have it be a difficult transition from a trust and integration standpoint. Interject some real disagreements between Janeway and Chakotay more like what we saw in Scorpion 1 & 2 but ramped up.
Have it be a difficult transition from a trust and integration standpoint. Interject some real disagreements between Janeway and Chakotay more like what we saw in Scorpion 1 & 2 but ramped up.