The war ended with Japan making peace with the allies, continue to exist peacefully with the US but has a standing army instead of a self-defense force. In other word, the mangaka's ideal nation (at the end of every volume, the mangaka comments on what he thinks is the ideal Japan, and this manga pretty much illustrate that).
As for the characters, the entire Mirai ship crew died except for the vice commander (i.e. the main character). At the very last chapter, 60 years after the war ended, a new aegis type Mirari is deployed with all of the crews being identical to the original... except for the vice commander, who is still alive and sees the ship sets sail.
That's the basic gist of the ending, it will take awhile to go into all of the details.
Dead as well, along with the flagship Yamato. His nuke did successfully go off thus forcing a ceasefire between Japan and US and he left the future of Japan in the hands of Yosuke. So yea... you could say he was the winner at the end.
Here's an answer I found on Y!Answers. All credits go to some guy who apparently was suspended from Y!
*Yamato sinks with Da Bomb on board after getting hit in its magazine by two missiles fired by the Mirai
*Da Bomb explodes in the bottom of the ocean, causing no significant damage, but is enough to warn the Americans the Japanese has nuclear capabilities
*Mirai is lost with all hands after a single stray hit by a shell fired from the American ships, the remaining crew are presumed dead drifing at sea and deliberately not rescued by either the Japs or Yanks
*IJN commander dude dies after getting dragged into the bottom of the sea in a vortex created by the sinking Yamato, already suffering from a massive head injury during the explosion of the magazine
*JDF commander dude lives but is crippled, he is picked up by the Americans, and does a deal with them after having been convinced by IJN dude before he died to help his cause to build "Zipang", knowing that he can no longer return to his own time since he technically cannot exist as his own father "died" as a child as an indirect result of the Mirai's existence
*The 1944 section of the story ends as JDF dude is transported to Washington on a stretcher on board a B-29
*Story the flashes forward to 1957 in Nantucket Island, JDF dude is now a very rich man through guiding America with his knowledge of the European theatre, and profiting from the post-war boom, though he is wheelchair bound. It is 13 years since the Japan-American peace treaty and 10 years since the formation of the Pan-Pacific Treaty Organisation (think NATO), Japan has agreed to give back all colonies and lands annexed, Mainland Japan has not been attacked and is prosperous as we know it. The pro-war factions of the army and the navy, as well as the government are ousted from power (over just 1 page - a bit simplistic) and the Japanese military is reformed and becomes the JDF in 1945
*Story then flashes forward briefly to 1970, JDF dude returns to Japan, one of the ex-IJN commanders that helped the cause is running for Prime Minister
*Story then flashes to 200X at the christening ceremony of the Mirai, a bigger, more advanced ship than the original, JDF dude, now an old geezer, has his staff gather information about his ex-crew members, who are all crew members of the new Mirai, and finally realises why only he gets to survive from the original Mirai - you cannot have two of the same person existing at the same time. So his father dies as a kid and he would not be born in this alternate timeline, while the rest of the crew all "die" before so they can be born again 20-30 later as history intended. The crew members, even though they don't know JDF dude, somehow gets the strange sensation that someone is missing among them
*The story ends as the old man waves goodbye to the Mirai on its originally-fateful journey, only this time, it suffers no mishap on its way and reaches its destination for the joint military exercise with the American Navy - only the old man knows how things could have turned out
I was once told on youtube that the Mirai was sunk with basically all hands. Supposedly there was something related to the Japanese developing the atomic bomb or something. And it was being transported on the Yamato(?) or something. Honestly take that with a HUGE grain of salt because its a youtube comment years ago that I can't even find anymore and we all know how trustworthy both the human memory and youtube comments are. I really don't remember and English translation never finished as far as I'm aware despite different groups picking it up but all dropped it again later.
If anyone have more information, feel free to correct me.
