Hear me out, I know a lot of people didn't like Salvation, but . . .
As the Sole Survivor, you come from a bygone era. You know war, and war never changes. When the War of the Machines starts, you have three options: Stay out of it, fight for humanity, or join Skynet. NOTE: PREFERABLY NEW FACTIONS, NOT INSTITUTE OR MINUTEMEN OR RAILROAD RESKINNED.
If you stay out of it, you remain friendly to both sides because they know you're too valuable to be killed. Skynet may try to kidnap you, still, or get close to you to gain your wisdom. Is that a red glow in your new romance's eyes?
If you join the Tech-Com Resistance, you will be recruited by John Connor's descendant, Riley Connor, to help strike hidden Skynet facilities in an attempt to shut it down for good, but you will be hunted by terminators. Skynet will even send a special unit, the shapeshifting and intelligent T-2000, to hunt you down. It could be anyone, so keep Dogmeat close to detect terminators, or use your terminator-detecting goggles. You can even hack a older terminator to pilot it into Skynet, to find the location of the central core!
If you join Skynet (becoming one of the Grays, in terminator canon), you will be cyborgified and turned into . . . basically Marcus Wright. You become the I-950 Cyberdyne Systems Model 001, with an enhanced skeleton, bullet time, enhanced HUD (like a pipboy replacer in your visor, similar to how the Power Armor helmet shows your inventory), and the option to have hidden blades and weapons in your arms (triggered by the grenade button so you can dual-wield). Heck, you can even install a neural chip and pilot terminator NPC's, even the t-1000, disguising yourself as any NPC- just be sure to kill them or imprison them so they don't come back and give you away! Your mission is now to kill John Connor and associates, or capture them so they can be similarly cyborgified, making them spies for Skynet . . . If you don't infiltrate the resistance yourself!
As a bonus, if the Resistance launches an assault of Skynet Base; what about a mission where you go back in time to a new map, whether as protector or hunter, to take out targets in the past- maybe including you if you're resistance, hunted on Judgement Day? And when the battle's won, if your side wins, you can return to your world- if not, as added incentive . . .
1. If you lose to Skynet, you will be cyborgified. Any move you make against Skynet, a terminator, or the Institute will result in death or losing certain skills (like even holding weapons . . .).
2. If you lose to the resistance, your inventory will be taken by the Resistance, and you'll be forced to either re-gather items from across the game or steal back your own from the resistance. Or you can re-earn it, but you have to kill every remaining terminator on the map.
3. If your past self is killed, you will return to the present with low health and on a lower level. Good thing you left your stuff in the present, it wouldn't have survived the time travel, much less the paradox!
And maybe as yet another bonus, you can seduce and romance a high-intelligence (later-model) terminator or a resistance member to the opposing side with side missions or a high enough skill check, or kidnap them with the help of a dart gun or termination knife.
Also, if you make this mod, please add all kinds of terminator lore stuff- maybe even the T-infinity or a pilotable HK Ariel? Hmm, I wonder if it's possible to build your own terminator companion with Automatron . . . Or infiltrate and silently kill the Raider leaders to destroy them from within?