Honestly, I'm completely flummoxed about where the story is going right now. The PERFECT time was about 6 months ago. Salvation had just shown up, Aegis was collapsing, the NMLA threat was bigger than ever, the Alliance Election was a mess, and Hudson was causing a mess with Yuri Grom and his surveillance laws.
Cut to the modern day and Aegis is gone(But nothing bad has happened), the alliance is basically back to standard political drama, the NMLA are all wrapped up, the Emperor is back without fanfare, most of Hudson's drama is swept under the rug, and Salvation is funding peaceful mining operations. All the drama has been allowed to just peter out.
You could totally have brought everything to a perfect climax, before. Reveal the NMLA and the Lords of Restoration, but have them attempt to seize power rather than being effortlessly eliminated. This starts a civil war in the Empire. Hudson attempts to take advantage of this and starts an invasion of the Empire, but overplays his hand and his dictatorial tendencies end up with his own civil war. At the same time, the Alliance, politically divided, threatens to fracture, and amidst the turmoil, Aegis collapses as its funding is cut off.
In the midst of all of this, Salvation fires his superweapon, wiping out the Pleiades and calling down a MASSIVE invasion of thargoids into the Alliance. The Alliance attempts to fight them off, but with Aegis defunct and many members refusing to send help, they are rapidly pushed back. They appeal to the Empire and Federation, but in the meantime Patreus and Torval have launched a counter-invasion into Federation space, and with the various wars going on, neither Superpower has the ability to reinforce them.
THEN you can bring in the missing emperor; have the players move to find her secret location! Every week, narrow the possible location a little bit, even as the thargoids push deeper and deeper into the bubble. Only she has the power and will to end the ridiculous war.
Of course, even with her returned, it will take time to work out a treaty that will allow the various Powers to agree to contribute much of their might, leaving their home systems defenseless. At the last moment, with the Alliance Armada under attack, you can have the Empire and Federation swoop in to save the day! Drive the thargoids back and emerge victorious!
Of course, if the players fail at too many things, it might seem hopeless. In that case, players would need to supply Salvation with enough thargoid materials to build a better superweapon, obliterating the thargoids but also wiping out all human inhabitation from the infested systems. A pyrrhic victory, by any means, but at least humanity would remain, licking their wounds and waiting for the next attack.
