Just so I can keep things straight, this is what I think happened, from Baron Blade's perspective.
During OblivAeon, BB sees that the tide has turned and since the world is no longer about to end, he doesn't need to hang around and get arrested. He fakes his death and bails with an OblivAeon Shard.
BB sees the Akash'Flora tree with all that delicious power and decides he needs it to power a new robot army.
He puts together a new army of minions and robots and sets up the undersea base near Megapolis. He builds the new robots in a way that it's not obviously his work, since he (presumably) wants to see Legacy's face when he returns in glory.
(The next few things don't necessarily have to happen in this order, but it makes the most sense to me.)
He gives some robots to Miss Information in return for her promising to use some of them to keep the Freedom Five busy when he needs a distraction.
He takes his Shard to Russia and sticks it in his old experimental generator as part of an alpha test of the Infernal Machine that's going to tap the tree's power. It does not go as planned and he bails, leaving the Shard in the reactor. (Then Proletariat shows up, hoping to shut down the reactor, but it makes his powers go wild. And then Fantatic shows up, making things worse.)
He goes to Insula Primalis to beta test his Infernal Machine and traps a spirit. (Presumably that's the small scale version of what he wants to do with Akash'Flora.) Now's he's ready to roll.
Side note: The stuff he did in Russia and Insula Primalis sets up a disturbance in the Void. The Voidheart starts trying to break through into our reality through Vanessa Long.
BB unleashes the first strike on the Akash'Flora tree and makes sure that he sends robots to target the F5 and Argent Adept.
Unfortunately, he (once again) underestimated the heroes, and they're able (presumably) to stop the Spider Mothership before it starts whatever it was supposed to do to tap the power of the tree.
Luckily for him, the Voidheart's attack on Vanessa Long happened at just the right time, and rather than take the time to track down the source of the robots, they have to go help Visionary.
(Presumed) Blade calls in that favor to Miss Information to see if she can distract the heroes for a little while, as he needs to fire up Spider Mothership 2.0 to crank out a larger army of bots. That's what he's doing while the heroes are flying all over the world.
Just before the heroes get back to Megaopolis, he unleashes Swarm 2.0, this time without a Spider Mothership right there for the heroes to wreck. And it doesn't matter if they track the signal back to the undersea base because he has so many traps and stuff that there's No Possible Way the Freedom Five will survive this time.
Does that sound right?