If it's a ship from the future then I guess that means they can't go back to the Federation without risking the timeline and changing events.
Chakotay being a captain of the Protostar doesn't suggest the far future though.
Could be that the Protostar was launched just a couple of years after VOY came back from the D.Q, and got stuck over 17 years into the past (remember that Diviner's bug terminator mentioned 'years' of failed attempts at finding the Protostar by others during the '17 years ago' sequence).
That would suggest the Protostar was flung about 20 odd years (maybe 25 years) into the past right after it was launched.
It could have encountered a temporal anomaly of some kind and wham... it was thrown into the past - this could have been done by someone during the Temporal Wars to prevent UFP from developing the Proto drive further... or it was just a random occurrence.
So, nothing would necessarily change for the Federation timeline-wise because even if the kids return to UFP in the next episode, the Protostar could have already been registered as 'missing' or 'lost' for a few years.
A bit of timeline:
- VOY was launched in 2371.
- VOY returned to Federation space in 2378.
- 2383 (5 years after VOY's return) is the year Prodigy is taking place (what we are currently observing).
- 2380 to 2381 could have been when Protostar was launched and shortly after ended up missing - gets thrown over 17 years into the past.
If we substract 17 from 2383, we get the year 2366 - this is when Gwyn was made (during TNG era - and ENT-D was launched in 2363)... but the dialogue suggests that many others tried finding the Protostar (and failing) for years up until that point.
So, based on what was said, the USS Protostar was thrown over 17 years into the past... possibly as far back as to 2363 (when ENT-D launched) or 2360, suggesting a a throwback of about 20-23 years... and fits into the timeline perfectly fine with the ship being searched for 'years' before Gwyn was made.
So, if we see a flesh and blood Chakotay in Prodigy, he will probably have grey hair and possibly some mental health related issues depending on what kind of environment he was in (probably not too fit to assume command so he will be relying on the kids to take him back to Federation space).
Speaking of which... that Transwarp jump of 4000 Ly's had the USS Protostar ending up in the Gamma Quadrant it seems... its possible Chakotay and his original crew ended up there... and could be prisoners of the Dominion (which would also tie into DS9, but its unnecessary to think this is how the Dominion got its info on A.Q technology because they had ample opportunities to take prisoners, capture ships and their databases from the first 2 years of the Wormhole opening - in fact, I actually think this is how the Dominion was able to have its polaron weapons bypass Federation shields... stolen intel basically from the first AQ species launching expeditions into the GQ in the first 2 years of Wormhole opening).
The holo - recording had recorded holo Janeway saying they are being boarded... that could suggest the Dominion, or another foreign power tried boarding the ship before Chakotay activated the Proto-drive in an attempt to keep it out of their hands (but not before he himself was beamed out), and ending up inside Tars Lamora.
Episodes are a bit short... but they make up for having a higher number of episodes in a season.
Will be interesting to see what actually happened (seeing how everything I mentioned is pure speculation).
