Okay. AlexChurchill thought LastExile was a very good series with a rather weak ending. It seemed far too DeusExMachina. For a series where most everything else has been carefully consistent, just what was going on in the final couple of episodes?
What was the deal with EXILE? Okay, it was originally a seedship carrying colonists from another world. Fair enough. And it's reasonable for it to end up in (creating?) the Grand Stream. I can even accept the tentacle-like defenses (although it's a real stretch to say they can knock out Guild ships but somehow only grab and slow down the Sylvana). But... what did the Mysteriums do? Why did Alvis have to be the one to speak them? And if she could do so while flying 500m away from EXILE, why not do so from a few miles away? Was EXILE carrying water - if so, why hadn't it deployed it earlier? Why would EXILE suddenly stop attacking things when one of the Mysteriums was spoken? What kind of remote control method is that, anyway - speaking four different codephrases handed down certain families for generations? Why did speaking one of them make it suddenly destroy its own tentaclish defense system, and turn golden? Why did it absorb Claus and lavi's fathers' vanship ten years ago?
EXILE was a colonisation/terraforming ship. After settlement, it was coccooned and its defences activated. A conversation between Dio and the Guild member taking care of Sylvana's engine implies that the terraforming features must be reactivated at regular, long, intervals in order to rebalance the planet's climate; and moreover, that a reactivation is due and that the current maestro has no intention of carrying it out. The activation mechanism fits this - four pieces of knowledge held by separate people and a physical timed key (Alvis's genetical makeup) combine to reactivate the ship. EXILE has a maximal range at which it can sense Alvis - you see that in the episode where Maestro reads out three of the mysteriums (which, incidentally, also make EXILE's friend-or-foe recognition recognise Maestro's ship as friend, although it carries on attacking other guild ships). Maestro mentions that Sylvana is also an original settlement ship that dates back from the same time as EXILE. Claus and Lavi's fathers' vanship was delivering a message to Dusis ten years ago carrying an offer of truce; presumably they flew too close to EXILE and activated its defences - certainly, in the flashback at the start of episode 1, they are surprised - suggesting that they were not expecting to encounter EXILE in the Grand Stream.
What was the deal with the Guild, too? I guess we're to assume that they ended up in control of some of the "original" seeders' technology, and decided to exploit it with things like the "unit"s. (Although being able to make the power source of a ship break free of its harness and fly out upwards... if Delphine could have done that at any point, and she was as capricious as we were shown, then why didn't she do that earlier?) Why would toppling the Guild's Maestro's ship stop some other Guild taking control of what Maestro had control over?
She didn't do it earlier precisely because she was capricious. By the time she did order all units pulled, some of them had been taken over by fighters in battles such as the one Moran got wounded in. The Guild units that got pulled returned to Maestro's ship, and were presumably destroyed when it toppled; the remainder were left split among the three factions, leaving no single group in control of all of them. Moreover, that was only part of the objective - the other part was to activate the terraforming ship.