As we know, the Silurians first appeared in the Third Doctors second story, Doctor Who and the Silurians (yep, thats the official name after the full script title appeared on the screen titles, rather than just The Silurians), also known as The Cave Monsters (from the Target novelisation). Later, in Pertwee's third season, their cousins the Sea Devils took their turn to try and reclaim the earth.
All went quiet under the earth until Davison's third season, when they both returned in Warriors of the Deep. Whilst the Silurian head design included the third eye, for some reason the script forgets about this ability. As far as the classic TV series is concerned, this was their last appearances.
In the Virgin New Adventures novel (number 19), the Seventh Doctor meets the Silurians in Blood Heat. Featuring the Brigadier, Liz and Jo, events turn out to be taking place in an alternative universe where the Silurians were successful in defeating the Doctor in the first encounter. There's a detailed story synopsis here. There's a whole host of crazy things that happen in the Virgin New Adventures, which I'm not even going to touch on here... have a look here for references and links (including other odd spin-off bits and bobs).
We also have the Silurians reappearing, this time including versions hybridised with Sea Devils, in the Missing Adventure novel The Scales of Injustice, with the third Doctor and Liz Shaw. Again find the synopsis here
This story is available online on the BBC Classic Who website which is available online here, together with some interesting artwork in the style of the Target series for the period, including a mock Chris Achilleos style cover.
And the Silurians again return in the Big Finish audio Bloodtide, with the sixth Doctor this time taking his turn to deal with some menacing Silurian scientists.
Doctor Who Weekly magazine ran a two part comic strip story Twilight of the Silurians, in issues 21 and 22. The story, which didn't feature the Doctor, was dedicated to Malcolm Hulke, who had died in May 1979.
The Doctor Who Monthly 1992 Summer Special features a story called City of Devils with Sarah-Jane and K9 (the only example of comic strip in this format, itself supporting the spin-off K9 and Company).
And then Doctor Who Monthly ran the story Final Genesis in issues 203 to 206 which again followed on after the events of the original Silurian story, with the Doctor again failing and being killed before alternative events unfold...
Doctor Who Magazine 516
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