It was a really Emotional and Beautiful Episode. Akecheta is awake for a Very very Long Time.
The Man in Black Lives
We saw at the very start of this episode that the Man in Black did survive his wounds received last episode.
Ghost Nation is saving guests in the here and now
The Leader of the Ghost Nation , Akecheta, finds the Man in Black near death by the river and saves him. He tells him he does not deserve the escape that death provides. This confirms the theory that the Ghost Nation are gong around saving humans, albeit with a somewhat darker purpose. They may also be hoping to get help finding the door.
How the Ghost Nation got the Maze Symbol
Akecheta wandered into the town with the white church following the original massacre that left Arnold dead. There he saw the maze game Arnold had shown Dolores, and became obsessed with it, and started putting it everywhere.
They majorly revamped the Ghost Nation storyline when the Park opened
The Ghost Nation/Native population of Westworld was peaceful and pastoral before the park opened. The writers turned them into killers so the guests could kill them without guilt in the early days of the park - before William visited for the first time.
What happened to Logan after we left him at the end of season one
He went pretty crazy; likely an effect of exposure and dehydration. Akecheta found him, and left him for the QA people to find. His babbling sparked recognition in Akecheta; he returned to his original home and realized he had once lived a different life. When Akecheta returned to find him, he was gone, and they were building something where he had been (maybe the Mesa, by the look of it?)
Akecheta has been aware of his reality far longer than we might expect
He would keep himself alive so that he would not be reset, and would not lose his memories of his family. He managed to stay alive for nine years. Eventually, he realized his only hope of finding Kohana was to die and be taken below. When the techs realized how long he had been out, they updated him without a full rebuild, which gave him the opportunity to see the whole lab setup and the rest of HQ.He found Kohana in cold storage, but was unable to rescue her.
Lee Sizemore might be marginally smarter than previously thought
When he insisted on saving Maeve last episode, many thought he had simply become emotionally attached. We now know that he recognized her ability to control hosts as a potential tool, and hopes to use her to regain control. He's also emotionally attached though, and didn't foresee them just breaking her down for parts, so judge him as you like.
Why the dealer had the Maze on the inside of his scalp
Akecheta had been carving the maze symbol into the inside of Ghost Nation scalps, where they could not be found and taken away by the techs.
Why the Ghost Nation attacked Maeve's homestead
It never really made sense that Maeve and her daughter would be attacked by Ghost Nation in their supposedly PG-rated corner of the park. The answer is that they weren't actually attacking. Akecheta was using the symbol to teach hosts of their own potential. He wanted to teach Maeve's daughter and keep her safe, which is why he came to the homestead.
Akecheta can communicate with Maeve through the mesh network
We see this at the end of the episode when he tells her they will protect her daughter.
Maeve might be able to access pretty much all the hosts stories
Her ability to access stories and dialogue of other hosts when she quotes Kohana at the end of the episode.