Captain Jonathon Archer is a fictional male Human captain in the Star Trek - Enterprise series. The character was portrayed on screen by Scott Bakula. His allegiance / loyalty is to The USS Enterprise NX-01. Archer is the first captain of the Starship Enterprise in chronological order. Although he has a mistrust in Vulcan, he gets along fine with T'Pol. Jonathon's company is a small beagle called Porthos, after one of Alexander Dumas's fictional Three Muskateers
Archer was allowed to recruit who he wanted for the mission. He recruited a Denebulan doctor (Phlox), Malcolm Reed as the armory officer, Cmdr. Charles Trip Tucker as the chief engineer, Hoshi Sato as the linguistic expert. T'Pol was fosted upon him and he believed she would be leaving after the first mission but she stayed.
Archer's first mission (Broken Bow) at the helm of the Enterprise was to return a stranded Klingon back to his homeworld of Kronos for which he duly congratulated for. However, the respect for him by the Klingons was not to last, Archer came into conflict with the Klingon many time and was captured and put on trial by the Klingons for assist an enemy. Archer was spared the death sentance and instead was punished to hard labour. He managed to escape with the help of his crew members.
Although the first recorded conflict with the Borg was during Captain Jean-Luc Picard time at the helm (Q Who), Archer did come against the Borg who had been defrosted after being found in the Arctic Circle. They had been part of the Borg Cube that had travelled back in time to kill Zefram Cochrane. (Star Trek VIII, First Contact)
Archer became unwillingly involved in the Temporal Time War. The Time War was when time travellers from the future were trying to affect the past. In Shockwave, he get catapulted into the 31st century where future has been corrupted so much that paper books has replaced technology. As the technology had not advanced enough, there was no way he could return but he comes up with a way to return.
When the Xindi launch an attack on Earth, killing millions, Archer is tasked with travelling into the Delphic Expanse where the Xindi are based and stop them before they destroy the Earth. After defeating the Xindi, he is catapulted back into the 1940's where the Nazi's are winning the war thanks to some dubious alien inventions. Only by destroying the alien technology can the timeline be restored.