This trophy is currently glitched and possibly unobtainable. If you haven't started Undermountain, it should be unlockable, but if you started but did not complete it before the patch in November, the in-game achievement and subsequently the trophy won't unlock.
I've submitted a bug report, so there's hope it'll be fixed, but if that is the case you will have to run an alternate account completely through the Undermountain and Uprising campaigns, and even then I've seen reports of it not unlocking.
During the Uprising campaign (continuating of Undermountain), you will have to go do daily missions:
2 Reconnaissance missions per day (Illithid & Githyanki)
Per 4 reconnaissance missions (2 per faction) you can do 2 Warden Expeditions (= ME's without collecting the 9 runes)
Per 4 warden expeditions (2 per faction) you can do 2 Fragment Expeditions (=Me's with a special final boss)
The two Fragment Expeditions' final bosses are what you are looking to beat with 3 runes attuned. Just like when doing Master Expeditions, attune 3 runes in the staging area and complete both for the trophy.
The Red Dragon Knight can be found in the Githyanki Fragment Expedition, and the Neothelid can be found in the Illithid one.