The Beginning of the ProjectModifier
Much of the Zanuka Project's progress was started when Alad V discovered a cache of sleeping Tenno near Sedna, which not even Lotus knew about. As the project went underway, General Sargas Ruk discovered Alad's trespassing and demanded that he hand over the cache to the Grineer, as it was unearthed in Grineer territory. Rather than complying with Ruk's demands, Alad strengthened the defensive forces stationed on Mars in order to flank the Grineer forces. Furious by Alad's defiance, Ruk then demanded that the Corpus hand over all their territory to the Grineer or else face severe consequences.
The commotion managed to get Lotus' attention, but she refused to sway the Tenno towards either side. Instead she left the Tenno with two options; support the Grineer in order to rescue their fellow Tenno at the cost of the Grineer gaining more territory, or support the Corpus and drive the Grineer away from Mars, sacrificing their fellow Tenno in the process. The following skirmishes would be collectively called The Gradivus Dilemma, being named after the first location to be contested.
After several engagements, the Corpus' Board of Directors decided to stop bankrolling Alad, on the grounds that the dilemma was putting a severe strain on their resources. With no resources to continue defending, Alad was forced to pull out and give the Grineer victory. The Board also cut their funding of the Zanuka Project as well, forcing Alad to continue the project without their financial assistance.
Despite the lack of funding, Alad was still able to make progress with his project, having relocated his research facilities to Jupiter. At this point, the Tenno caught word that there was a newly discovered Warframe in his possession that was being used for the project. Meanwhile, Alad's former colleague Frohd Bek was also tracking down Alad in response to the massive debt he owed the Board as a result of the Dilemma, though Bek also feared that his position would be jeopardized if the Zanuka Project is successful. To counteract Bek's searches, Alad diverted the Infested to his ships, overwhelming them in the process.
Frohd Bek presented a deal to the Tenno; clear the Infested from his ships, and he would give them Alad's location. Although Lotus showed distrust to Bek she reluctantly agreed to his stipulations, fearing that more Tenno would be killed if Alad was allowed to continue. The ensuing manhunt cleared out the Infested and revealed Alad's base of operations in Themisto. By that time Alad was able to construct a working Zanuka prototype, but despite this the Tenno were able to defeat him and rescue the remaining Tenno in his clutches.
Aftermath of the ProjectModifier
Although Alad was stopped, the Warframe he had in his possession had been extensively modified, leaving her physically and mentally scarred. Due to the lack of funding and resources the project's progress ground to a halt, but Alad was able to counteract this by developing Zanuka Hunters; downgraded Zanuka proxies that were easier to mass-produce.
Determined to see his project succeed, Alad would send these proxies to subdue and abduct Tenno during their operations in order to continue his project.
Behind the ScenesModifier
The Zanuka Project was revealed during Livestream 16, with Digital Extremes stating that they would like to add Warframe creation to the lore of the game (as most Warframes were produced during the Orokin era, making Valkyr a "recent" development). The Project also introduced the game's second assassin in the form of the Zanuka Hunter, who would track down Tenno who sided with the Grineer during Invasions.