While she's gone, the Doctor recovers from his coma, only to find that the doors are sealed shut and all the air is gone -- apparently because squirting plants outside have covered the TARDIS in their thick fungus (yeeesssssss... it's probably better to just screw your eyes up tight and accept for this story that an interdimensional time machine can be nearly incapacitated by plant juice than try and reason your way out of this). Fortunately, Jo Grant finds help from some space travellers on the planet ("I'm qualified in space medicine," Taron, their leader, tells Jo, but declines to mention what makes space medicine different from regular medicine) -- trying to avoid "them". Unfortunately, she's been squirted by those plants, and so now she's being slowly covered by fungus.
The travellers find the TARDIS and break off the fungus enough for the Doctor to get out -- good thing, too, as he was almost completely out of oxygen (remember, just accept this). He works out that these travellers are in fact Thals, as last seen way back in The Daleks. They're on this planet, Spiridon (pronounced ['spaɪ.ɹɪ.dən], or SPY-rih-don if you don't know IPA) on a secret mission, one that they refuse to discuss. The Doctor's also on a mission that he refuses to discuss, but at the cliffhanger it turns out they're both on the trail of the same thing: "Daleks," the Doctor says, as if he wasn't expecting them. Let's remember not just that this story has the word Daleks in the title, but that last episode we learned all about their plot to conquer the galaxy and that the Doctor headed to Spiridon (with Time Lord assistance) for the express purpose of stopping them. But no, the production team (or maybe just Terry Nation -- who's back writing a Dalek story for the first time since season 3 and The Daleks' Master Plan) has decided to hold back their appearance till the cliffhanger and pretend we won't know who the baddies are until that moment.
Still, at least we get something a little different: this Dalek is invisible, a trick it's picked up from the native Spiridons.74 Invisibility takes so much out of the Daleks though that this one is basically dead (or actually dead -- it seems to be the latter, but it's not entirely clear), so the Doctor and the Thals end up wandering the jungle avoiding Daleks (apparently there are about 12 of them on the planet) and bands of invisible Spiridons. Not entirely successfully, though: Codal, one of the Thals, runs off to distract the Spiridons and ends up being captured by them.
Jo, meanwhile, is succumbing to the fungus. She attempts to leave the Thals' ship but collapses nearby. And then the Daleks come to destroy the Thals' ship. The Doctor, believing Jo is still inside, rushes out and tries to stop them, but the Daleks paralyze his legs (yes, just like Ian in The Daleks) and get on with blowing up the Thals' ship before capturing the Doctor and taking him to a small cell in their base (yep, again like The Daleks), where he meets up with Codal (all right, that's different). He gives a little speech about bravery and then it's time to try and escape. And while this is happening, Jo's fungal infection is treated by a friendly Spiridon.
But the game-changing moment occurs near the end, when another Thal ship crashes down on Spiridon. One of the survivors, Rebec, tells Taron that there aren't twelve Daleks on Spiridon; there are 10,000. Which is actually a pretty good cliffhanger and goes some way towards making up for that lousy first one.
74 Although the less charitable among you will note that Nation also has invisible aliens in The Daleks' Master Plan (specifically the fifth episode, "Counter Plot"). No invisible Daleks though.