Modern N. Trophy is nothing like his classical self and is much darker and keeps himself to himself and has not been seen for years since the events of Crash Nitro Kart and has remained mobile and his relationship with Cortex deteriorated in Twinsanity when Cortex was working with Crash Bandicoot. However as the years went by Modern N. Trophy was approached Modern Cortex who wished to repair there friendship and form a partnership to finally defeat Crash Bandicoot by going back in time and teaming up with there past selves. Modern N. Trophy agreed and helped Modern Cortex by opening up a time vortex and going back in time with him to the Post Twinsnaity era and forming an alliance with there past selves.
Modern and Classic N. Trophy then created a warp room in hyperspace linking to past locations and were the ones pulling the strings and keeping the entire plan intact and kidnapped all of Modern Crash and Classic Crashs family and friends.
In Crash Bandicoot Past and Future Modern N. Trophy and Classic N. Trophy controlled all of the time vortexs and were the ones who orchestrated the entire plan/scheme. Modern N. Trophy and Classic N. Trophy showed up towards the end to confront both Modern and Classic Crash and shattered the level they were in and slowed down time and pulled both of them into the heart of the time vortex. Modern N. Trophy battled Modern Crash but was defeated along with his past self who was defeated by Classic Crash and the vortex collapsed and blew up within itself. Luckily the vortex spat out both Modern and Classic N. Trophy who both were damaged and when Modern/Clsssic Cortex were defeated and the universe was restored it is not known what happened to Modern N. Trophy though his past self went back to his own time but Modern N. Trophy is still a threat and could show up again.