This episode basically puts the Justice League on the defensive. They strut their stuff early on by breaking out of prison, but are quickly driven into hiding as earth falls under martial law.
The irony is that for all their efforts throughout this episode, the League's efforts are for naught when Hawkgirl (somehow) leads the Thanagarians to the Batcave, setting the stage for the finale.
Thankfully, it's Wonder Woman, not Batman, that engineers the League's escape. But the League quickly display the lessons on teamwork they learned back in "Secret Society" and cut loose, making their way out of the ship and back to Metropolis. From there, there is the revelation of what few secret IDs remain in the League, and finally the determination (despite some apparent discrepancies in "Brave and the Bold") that the League's Flash is red-haired Wally West.
We then get a bit more of the Batman/Wonder Woman romance as they are forced to fake (?) some passion to maintain their cover. Clark/Superman gets a few moments to use his brains instead of his brawn. And finally the League meet at the Batcave where we return re to where it all started - with WB's animated DC roots in the Batman: Animated Series.
There are a lot of little character moments and one good fight, but this episode's focus is more on establishing the stage for Part 3 - we see more of martial law under the Thanagarians, some necessary establishing material. Nothing earth-shattering here - we'll get plenty of that in Part 3.