Well, the Sontarans are really close to poisoning everyone on Earth. That would be bad. Of course, most of humanity will have forgotten all about that in a couple of episodes one way or the other.
That said, the important thing to remember with the Doctor is he is always more on top of things than he appears to be. So, even if Col. Mace of UNIT is really close to launching nukes at the Sontarans, something the Doctor assures him will not work, and even if there’s a Martha clone in there sabotaging whatever it is Mace and UNIT are trying to do, that doesn’t mean the Doctor doesn’t have a solution to all this.
Part of it does come by accident. The Doctor told Donna to wait in the TARDIS, and Martha-clone had her brainwashed people teleport it to the Sontaran ship as a trophy. As such, the Doctor can get a lot done by calling up the Sontarans knowing the real message is for Donna in the TARDIS. And as Martha-clone keeps stopping the nukes from launching, and as UNIT regroups with weapons that actually can kill a Sontaran after they massacred a bunch of soldiers to start with, the Doctor slips off, finds the real Martha, and reveals he knew the other one was a clone the whole time thanks to small differences only he could have possibly noticed. He also knew she was stopping the nukes from launching which was why he didn’t say something sooner.
So, with little better than a mobile phone call to Donna, the Doctor is able to get the TARDIS back, find the humiliated Luke Rattigan (what a surprise, the Sontarans lied to him), and even figure out why the Sontarans, who pride themselves on military might and courage, would use a poison gas attack against a population they weren’t actually fighting.
Short answer: the gas’s removal of humanity was just a bonus. It was really there to act as a nutrient for Sontaran clone vats as it would turn the entire planet into a cloning facility.
That’s…very Sontaran of them.
So, the Doctor builds a gadget to clean the air with a big fireball, then teleports to the Sontaran ship to tell them to go away or else, but Luke zaps up and takes his place. The Sontarans in orbit explode, UNIT takes care of the ones on the ground, and while Mace was getting a little tired of the Doctor constantly telling him to stop doing what he was doing, I still got a hint of a little respect for the Doctor when the Doctor said he wished the Brigadier was there and followed up with a “no offense,” to which Mace replied, “none taken,” suggesting he wouldn’t have minded Lethbridge-Stewart being there either. Then again, even if UNIT returns, we may not see Colonel Mace again regardless.
So, that’s that. The real Martha goes to thank the Doctor and Donna for their help on the TARDIS before reminding the two of them she’s engaged to a very lovely man when the TARDIS doors slam shut and the ship starts itself up and zaps itself away into some other part of time and space against the Doctor’s will.
So, yeah, he has two companions now. But did I see a flash of Rose at one point in time or another? I thought so. Must be the final series for this Doctor then if all his companions are coming out to play.