Well obviously looking at the ending scene in Volume 42 there's a lot of speculation to be drawn. So maybe someone should make a thread about it? I'll state my theories to get things going.
We can see that Pryce is here, somehow in present time. I think we can owe Pryce's return to Celebi. Maybe what happened is that Yellow was in the Ilex Forest with Gold's Pichu (it's not in his party right now so it has to be somewhere) and she encountered the Spiky-eared Pichu. And then Celebi shows up and warps Yellow back in time where she encounters Giovanni in Tohjo Falls listening to the radio when Team Rocket takes over Radio Tower (when Carr is in charge of Team Rocket earlier in the HGSS chapter). Yellow convinces Giovanni to bring a halt to Team Rocket's evil plans (she talks about how his son wants to cover up for Giovanni's crimes like he said in FRLG) so Giovanni goes with Yellow to present time with Celebi. Along the way they encounter Pryce in the voids of time so the two take Pryce with them due to his reformation. So that's why Giovanni is there with Pryce. Just a theory (most likely not true but it may be along the lines of that).
And also, notice how grim the three former villains are looking at the end of Volume 42. What I noticed is that if there is no more to the plot than we know then there is nothing to be grim about (and certainly no reason for the three enemies to group together). The point of the Arceus thing was to bring Giovanni back. If Giovanni is back and he wants Archer to stop his insane plans, then he could just tell Archer to stop and everything would be fine. What I think is going on has three possibilities: one, Archer officially lost his mind, lost sight of his original intentions and now he will attempt to take over the world with the most powerful Pokemon in the world. Two, since Arceus lost faith in humanity, it will try to destroy humanity completely and that is the problem that the three villains are worried about. Three, there is a greater evil behind the Rocket plot. Some villain that we saw before told the generals that Arceus will bring Giovanni back and so the creation process is all according to plan and the greater evil will swoop in and do his/her thing with Arceus and the Creation trio. The three ex-villains are aware of this and are there to stop the greater evil's plans.