This fanfic is a short story sequel to the fanfic WHO:1999.

Terrible noises of explosions and flashes of blue light could be heard and seen respectively on the viewscreen in the TARDIS.

There were three men in the TARDIS at the time. A young man, with short wavy hair, wearing a long green velvet jacket, a waistcoat with a pocket watch and a cravat, looked quite worried at the current happening. 

“I couldn’t have imagined this would have happened. Or have happened now.” the man uttered. He was the Doctor, his Eight Incarnation now.
He had been to another universe where he had picked up his two current companions, Paul Morrow and Professor Victor Bergman. They had just entered the Doctor’s Universe-777.

Passing through the Vortex, the TARDIS had breached the inter-universe barriers and as soon as they arrived in the Doctor’s universe-777, they witnessed an explosion in the Vortex.

“Does this happen often?” Victor enquired. His scientific studies hadn’t prepared him for what he was experiencing.
“No! The walls of the multiverse have deteriorated!” the Doctor exclaimed.
“Was it our fault?” Paul asked. “Did we cause this ourselves by coming here?”
“No of course not, I’ve been doing this for ages untold. The Time Lords – they are my people – being present allow travel to parallel dimensions. They keep open the pathways. Something has happened. There is a “storm” in the “pathways” right now.”
“A storm, Doctor? What kind of storm would that be? A temporal storm?” Victor asked.
“More of a warstorm. A warm is brewing. I knew it had started. It has been for quite a while now. It started on Skaro a long time ago, it’s the home planet of the Daleks. They are the enemies of the Time Lords. Or on BeretWorld, an interdimensional nexus.

Well there already was another Time War before, but this.. this will be  = no this is = worse, much worse.”
“Can’t you go back in time, Doctor? Stop it from happening in the first place.” Paul asked.
“I can’t go back in my personal timeline. And the Time Lords will be trying all they can”, the Doctor answered. “It doesn’t seem as if I will be able to take you back to where you came from. Or returning back to your universe any time soon.”
“It’s not as if we had much to look forward to. Our earth was dying in the future. Our moon’s resources were going to start to dwindle soon, we had an uncertain future in space”, Victor said.
“I’m really worried. What are we going to do now?” Paul asked.

“I’m not a Man of War. I will do my best to bring peace. As much as I can.”, the Doctor answered.

The story takes place in the Doctor’s universe-777 which is the same universe in which JJ Abrams’ Star Trek (2009) movies occur. The story of the first Enterprise may have happened differently in the original Star Trek universe.
The Sargasso sea of Space with its derelict spacecraft is taken from Space:1999 (The Cellini episode) “Dragon’s Domain”. Thanks for that great episode.
Star Trek is (C) by Paramount;
Doctor Who, Amy, Rory, the Daleks are (C) the BBC.

My understanding is that the last great Time War took place towards the end of the Eight Doctor’s run in books/audios/comics. Thus the Doctor’s crossover with Space:1999 occurred in that time period.