That secrets are the common theme in every subplot in this episode is itself no secret. Early on, Don asks Sally, "Can you keep a secret?" Later, in bed with Henry, Betty says, "I don't want any secrets" while neglecting to tell him, a man defined by political ambitions, that she, his wife, has just lied to federal agents. In their elevator conversation, Pete answers Don's anxiety with "If you're asking if he knows how to keep a secret, he works for the Department of Defense." -- a line which presumes that Pete's friend is more devoted to hiding the truth than to his employer and nation.
If factually informed, as by Doctor Faye's research, this episode might be a tutorial in lying. It's not just that the characters in this episode have secrets. They lie more when they're caught. They lie when they talk about others' lies. Don smiles at his investor's suggestion that he's sleeping with Megan, because that's a scandal he could share with the boys -- and yet it's not true. Joan, anonymous at the abortion clinic, still lies to a stranger and says that she's there for her nonexistent daughter. Pete, who has kept two affairs -- one tinged with blackmail -- from his wife, grouses to her about how liars make life difficult for "honest people" -- a valid complaint, but Pete needn't worry because he doesn't know any.
The news of Lucky Strike's imminent defection is Roger's business-related secret, while Joan's pregnancy is the more immediate of his social secrets. That he suggests that he might leave his wife for her is another. He leverages Lee Garner, Jr., a man with significant lies in his life, into giving SCDP more time by reminding Lee of "all the lies I've told for you." Lee needn't worry too much about the debt incurred when Roger lies for him: Roger's lies come very cheaply. Later, Roger voices sympathy regarding the death of a client while callously thumbing through index cards for his next call. Wishing out loud -- in front of the man's wife -- that Greg not return alive from Vietnam, Roger shows an almost sociopathic lack of care for anyone who's not him.
Lane has "gone native" in his new home, bearing a Mickey Mouse with red-white-and-blue balloons as a gift, when he expects his son but is met by his father. Lane has a secret girlfriend, who happens to be African-American as well as a Playboy Club bunny. To validate the care with which everyone else guards their secrets, Lane finds out that a cane across the head is the penalty for being found out.
And we are reminded that Don has more than reputation or a caning at stake should his secret past be found out: He is also guilty of desertion, a crime with no statute of limitations, and could face jail time -- in principle but not in practice, even the death penalty -- for a crime. He is rightfully grateful to Betty for hiding his secret. And for following his tactic of further evasion, as Don speaks elliptically once she suggests that they cannot speak freely over the phone. Pete seems to be savvy to this point, meeting Don in person and specifically avoiding the use of the phone. In so visiting, Pete sees Faye departing, and so finds out another secret that he claims he would have preferred not to know. Given the extreme lengths to which he went to find out Don's bigger secrets, this seems itself to be unlikely. Counter-truth tactics are second nature to everyone. Joan and Roger also switch to "code" when she opens his office door. Don and Faye do the same, to cover their relationship.
Finally, when the partner meeting takes place, Pete lies to explain why North American (fictitiously) fired SCDP. Roger, harboring a much bigger lie, berates Pete before giving a thumbs-up to describe business with Lucky Strike.
As the main action ends, Don eyes Megan with obvious intent. Joan's strategy to keep Don from his baser instincts lasted only as long as Miss Blankenship's heart held out. Don is ready to fall again. In keeping with the rest of the episode, this is an impulse than Don keeps, for now, to himself.
All of these private secrets come as second nature to the characters perhaps because their lives are built around secrets. As they propose an approach to advertising for the company that builds missiles ("You never need to say the word 'bomb'"), they scheme up an approach that doesn't mention missiles. The company's report is comically redacted with more black rectangles than it has words remaining. The exec from North American aviation addresses the black rectangles by saying "There'll be fewer black bars as the process moves forward." This prediction, not surprisingly, proves to be false.