Now tell me if God incarnated and came to earth then who was controlling the skies and matter? Also, also you said that Prophet Jesus (pbuh) died, if He is dead it means God is dead as well, and if this is the case then who is controlling the universe as there is no god left? Also you said Prophet Jesus will come again. How will He come again as God and Prophet Jesus (pbuh) both died?To answer this question, there are two things we must understand. First is the nature of death. James says, "For just as the body without the spirit is dead, so also faith without works is dead." (James 2:26) Death is not extinction but merely separation. When we die, it's not that we cease to exist, rather it's that our body and our spirit are separated and the fleshly part of our life dies and our spirit lives on. Our body is temporal but our spirit is eternal and lives on eternally even after our death. Even the Koran testifies to this truth.
"God takes the souls [unto Himself] at the time of their death, and that which has not died, in [during] its sleep." (Koran 39:43)
"Count not those who were slain in God's way as dead, but rather living with their Lord, by Him provided [richly sustained], rejoicing in the bounty that God has given them, and joyful in those who remain behind [follow after them] and have not joined them, because no fear shall be on them, neither shall they sorrow," (Koran 3:164-165)Furthermore, the scriptures make it clear that the dead are not unaware, but fully alive and able to perceive, feel, and communicate. Jesus tells the story of two men who died and their very different experiences after death. "Now the poor man died and was carried away by the angels to Abraham's bosom; and the rich man also died and was buried. In Hades he lifted up his eyes, being in torment, and saw Abraham far away and Lazarus in his bosom." (Luke 16:22-23) When asked about the resurrection, Jesus said, "But regarding the resurrection of the dead, have you not read what was spoken to you by God: 'I am the God of Abraham, and the God of Isaac, and the God of Jacob'? He is not the God of the dead but of the living." (Matthew 22:31-32) Truly, those who die live on, just not in this world. This is why the scriptures speak of those who are "cut off out of the land of the living." (Isaiah 53:8) Still living, just not in the land of the living. Even though Jesus died on the cross, He still lives, both as God and man.
The second thing we must understand is that God is not limited by human or physical limitations. God is the one who fills all things. Paul says, "He who descended is Himself also He who ascended far above all the heavens, so that He might fill all things." (Ephesians 4:10) God is everywhere at all times. David knew this and said, "Where can I go from Your Spirit? Or where can I flee from Your presence? If I ascend into heaven, You are there; if I make my bed in hell, behold, You are there. If I take the wings of the morning, and dwell in the uttermost parts of the sea, even there Your hand shall lead me, and Your right hand shall hold me." (Psalms 139:7-10 NKJV) God is able to dwell in human for in Jesus Christ and still fill the universe He created and controls. Paul tells us that Jesus "emptied Himself, taking the form of a bond-servant, and being made in the likeness of men." (Philippians 2:7) Jesus emptied Himself but He didn't empty heaven. Whether embodied in Jesus Christ or filling the universe He created, God is still in control.
I hope this helps.