Okay so jump back to the cold war, the UNA invented a bio weapon called the Technocyte Virus and sent a submarine loaded with samples to a Russian Island to perform tests. A scientist went rogue and the Agency had to send Hayden Tenno to eliminate him but there was complications and Tenno ended up infected with the virus. However unlike in others who went insane and became a monster made of a mix of techno-organic flesh Tenno's arm was the only thing that was mutated into an organic alloy that could create a glaive for him to throw. As he continued the mission he would find another women who had the same reaction to the virus as him wearing a prototype warfare of the Nyx, and also pickup another prototype of the Excalibur. When he completed his mission he went on to find others who could adapt to the virus as well, displaying reactions to their Alloy body parts like shooting flames from their hands or super human strength.
The virus also spread over earth, changing the fauna and animals.

Forward a few thousand years the solar system is under the control of the Orkin, an AI/Robotic or transhuman race the ruled the solar system for a number of years. The Infested were a blight on the solar system, consuming world after world so the Orkin used the Tenno who were immune to the virus to fight them, improving their warframe designs to make them the ultimate warriors. 
However after the war against the infested the Tenno turned on the Orkin, Lead by an Orkin named Lotus they freed humanity from their rule and Lotus then commanded the Tenno to go into cyro sleep in-case they are needed again in the future.

Forward another 1000 years and the solar system is in turmoil, the Corpus and Grineer have expanded to take most of the known universe and are on the brink of war, also with the rise of the Infested coming back Lotus who has been dormant for all this time awakes and retrieves the Tenno, waking them up to restore order to the galaxy and once more defeat the Infested.

My idea for the setting would be that our Tenno Clan awakes on a Orkin Dialect. At the same time another squad of Tenno are breaching it hunt for artifacts, our Tenno however are left without a guidance of Lotus and seeing the ship in battle mode their instinct kick in, going into defense mode they fight off and kill the invading Tenno squad and as a result they are branded as Stalkers, forced to flee on the dead Tenno`s ship and try and survive in the warring galaxy.