So we're starting season 4 (though The Smugglers is actually the last story filmed as part of season 3), but we're picking up where we left off at the end of The War Machines, with Ben and Polly pushing their way into the TARDIS. The telesnaps hint that the last scene of The War Machines might have been played in over the theme music before going back to the titles -- obviously it's hard to tell, but, at least as they're displayed in Doctor Who Magazine Special Edition #34: The Missing Episodes - The First Doctor (to give the publication its full title), the impression is one of title sequence, scene, title sequence (and certainly the theme music runs much longer than normal, supporting this).
But Ben and Polly barge in, pointing out that the Doctor dropped his key, so they used it to get in (and just to reiterate, this isn't a goof as is often claimed; it's not Dodo's key, it's the one that fell out of the Doctor's cloak in the previous episode). But the Doctor states that he's already moved the TARDIS, and so there's no telling where they are. It takes a bit of convincing, but eventually Ben and Polly believe that they've been transported to 17th-century Cornwall, full of thieves, smugglers, and ships crewed by men of ill repute. Yes, it's Doctor Who's pirate story.
It's got to be said, Ben and Polly sure do adjust to having been taken back in time rather quickly. There's no extended period of disbelief, like Steven had. Instead it's "Well, guess we really did travel to the past, then." This means that they can launch themselves into the proceedings without too much angst; indeed, Polly seems to treat it as a big lark, while Ben seems more concerned about making it back to his ship on time. But it doesn't take long for the Doctor to be captured by pirates who are convinced he knows something about a hidden treasure, and for Ben and Polly to be framed for the murder of the churchwarden. They're thrust into a terrifying situation, cut off from their own time and place, and the only person who can get them back home has been taken to who-knows-where. Ben and Polly cope with this, er, quite well, actually. They don't seem terribly concerned about the murder charge, and they're more interested in finding the Doctor so they can leave.
Episode 2 shows the Doctor in charge, wrapping Captain Pike (leader of the pirates and owner of a metal pike in place of a hand) around his finger. Well, maybe. There's a suggestion that Pike's toying with the Doctor as much as the Doctor is toying with him, but before Pike can begin to lay into the Doctor, he's interrupted by a new arrival. It seems there's an opportunity for some smuggling to be done...
Meanwhile, Ben and Polly, displaying a surprising amount of resourcefulness, trick their jailer into thinking they're witches who've taken over his soul and will kill him unless he lets them go. Then they go back to the church to look for clues into the warden's murder. They don't find any clues, but they do find a revenue man named Josiah Blake, who has tracked the smugglers to the church crypt. They tie him up, thinking he might be connected to the murder, and Polly goes to tell the Squire. Only it turns out the Squire is in on the smuggling, and isn't going to let a stranger tell her that his new-found compatriots Pike and his crew are involved in anything dodgy (as Polly recognizes Cherub as the man who kidnapped the Doctor). But he will lock Polly and Ben back up in jail...
So the thing about these first two episodes is how entertainingly unsophisticated they are. There's none of the nuance of The Massacre to be found here, nor much of the humor of The Gunfighters. Instead this is more a literary pastiche, recalling the works of Robert Louis Stevenson, as well as J. Meade Falkner's novel Moonfleet. This means it moves along at a relatively fast clip, wasting no time exploring the morality of Captain Pike or of the Squire. Pike and his men are pirates, so therefore they're not to be trusted, and the Squire is in league with them, so he's no more trustworthy than anyone else. The only one who seems to have a glimmer of morality is Joseph Longfoot, and he's killed for his sins by Cherub in the first episode (in one of the few remaining clips from this serial -- funny how some of the most violent and terrifying moments that were deemed unsuitable for broadcast in Australia and New Zealand are now all that remain of these episodes). Ok, and maybe the innkeeper's helper Tom, but he's portrayed as fairly thick and thus a figure of fun at Ben and Polly's expense. No, this is an uncomplicated tale (despite all the treachery on display thus far), and there's nothing wrong with that. It makes for entertaining listening at the very least.