Quake

Key information first. You need to start a New Game for this. Doing it from level select won't give the trophy (from what I have read). You don't have to unlock the secret levels if you don't want to. I personally went through all secret levels since I did a full run for all the trophies.

To unlock nightmare difficulty, start your game, pick any of the difficulty and then walk through to episode 4 on the right. You will come to a pool of water, look down drop into it and immediately hold back. This will allow you to float, rather than fall straight through. Look for the wooden beam below and aim for it before going through. After landing on the beam, head through the gap in the wall and through the portal. This will set the game to nightmare difficulty. Video linked for process to unlock it if you prefer to follow the method, rather than read.
To get this trophy, you have select New Game > Quake campaign and play through Episode 1, 2, 3, 4 and the final boss room on the nightmare difficulty. You can save as often as you want so it is just a case of trial and error. What I would do is at the start of each level, I would make a proper save, and a quick save. I would then push through the level and if after each fight I felt I ended with a good amount of health and armour, I would do another quick save. If you quick save in a bad spot, you can either die and let the level reload at the start, or use the proper save. I would save each level as a new save until I ran out of slots, and then start overwriting the oldest. I didn't need it, but the idea was to have past options if I ended up with too low ammo or health to progress.

Use corners for cover when you can. Try to remember ammo and health pick ups when you are full. That way you can backtrack. You carry everything over to the next level, so being prepared is always smart. Nothing carries over between episodes though, so when you are nearing the end, use your most powerful ammo. If there is a quad damage pick up, I would make a quick save before grabbing it. I could then scout out the best route to use it. If I wasted a lot of time going to where there are no enemies, I would quick load and use it smarter next time.

I used the following guide to get all the secrets. This was key as they contained the best armour pick ups, quad damage, spare ammo, etc. Without that, I could see this being a much bigger struggle. https://steamcommunity.com/sharedfiles/filedetails/?id=62089...

There are 2 trophies connected to nightmare mode you might want to work on as you play through. The first is doing a run of the first level without firing a gun. Your melee weapon is fine to use though, so I would say to just take it slow and kill enemies as you go. Use cover etc, and use quick saves. That gives The second trophy is towards the end of the game is on the level E4M6 The Pain Maze. You have to do a run without taking damage. Utilise quick saves and tracked your health and armour before saving each time so you know it is safe to continue. Doing so gives I used the following video to help with The Painless Maze