A/N: for full Disclaimer see the bottom of the chapter. This crossover will pick up form when Shinji and Co. landed aboard the Over the Rainbow and from there well let's just say that the laws of time and space can be a real bitch. But first, a little prologue to wet everyone's appetites as I have never seen a crossover like this done before.

Neon Genesis Evangelion: Chronicles of the Companions

Prologue: A Warning to the Foolish

Kozou Fuyutsuki found himself in the cavernously frightening yet all too familiar office of his former student and present employer Gendo Ikari. Fuyutsuki was already aware that both Evangelion Units 02 and the recently completed Unit 05 as well as an 'item of disreputable origin' were en route to NERV today so why was he being brought here he wondered?

"Fuyutsuki, have you read the Profile on the 4th child that the British government sent us?" Ikari asked in his calm yet intimidating voice.

"Yes I have and I must say that despite the fact that he's still in school the 4th child's mechanical, technological and, overall scientific aptitudes were instrumental in the early completion of Unit 05 and the modifications he made have even given Dr. Akagi pause." Fuyutsuki responded impressed.

"And your opinions of physician and tactical advisor that are arriving with him?" The Commander asked.

"Do you want my answer based of the 'official' records or the dossiers from the council you gave to me?" Kozou retorted. To which the commander only glared. "Frankly I'm surprised that either organization hasn't tried to infiltrate us sooner. On that note do you think that the 4th and our 'associate' are in their loop?" Fuyutsuki asked.

Probably not but I highly doubt that will stop either of them from looking for answers to rather 'unsavory' questions. Having said that, it is unlikely that Section-2 will be able to cope with our more 'unorthodox' infiltrators though they might be able to stall Mr. Ryoji and the 4th to a certain extent. Yet, I may need the others in place as bait."

"Bait?" Fuyutsuki asked intrigued.

"Rei came to me a few weeks ago and told me of a strange encounter she had. She was coming to NERV for Unit 00's reactivation test when she was approached by a blond woman in her early twenties with a thick English accent and she asked her to pass a message on to me."

"What was it Fuyutsuki interrupted."

"She said; Don't try to play god, you are tamper'n with forces way outside of present human understand'n and if you're the one caused what is happen'n it will be the end of everythin'. Also if you meet an unusual man with sorta messy brown hair, wear'n either a blue or pinstripe suit give him message from me it's jus' two words."

"What were they?" the Sub-Commander asked perplexed by what he was hearing.

"Bad Wolf" Gendo answered.

"Now assuming that Rei is telling the truth or that it simply wasn't a figment of her imagination, what dose this all mean?" Fuyutsuki asked

"You know as well as I do that Rei is incapable of lying and lacks the imaginative capacity to create something this complex. As for meanings the phrase 'Bad Wolf' appears randomly throughout history and according to Chaos Theory there is a reason for that we seem to be incapable of understanding. As for this 'Oncoming Storm', Keel informed me that he is a being of considerable power, cunning and, intellect also, he may even be more dangerous than all the angels combined." Ikari stated.

"Then am I to assume he is a threat? Also, what dose this have to do with the new staff?" Fuyutsuki added.

"To both the scenario and ourselves to be certain, as for our new staff, it has been mentioned to me that he has had traveling companions in the past that may have means to communicate with him." Ikari added cryptically.

"I see, is that all?" The Sub-Commander asked.

"For the moment, you may go." The Commander responded

With a long creek followed by a click and several automatic locks Gendo Ikari pulled a key from his suit pocket and unlocked a drawer in his desk and looked carefully into it. There in the drawer held the picture of his late wife, Yui holding there then eighteen-month-old son while wearing a strange pendant over her neck. Also, in this drawer was said pendant along with a pocket watch both engraved with similar patterns of concentric circles.

When he closed the desk Ikari became lost in thought; "I will not allow everything I have set in motion to be undone, fools all of them SEELE has no idea what I have in store for them. As for UNIT and Torchwood they are but fading lights in the darkening world and will be snuffed out by the dawning of the new one. I can't be stopped now not by them and certainly not by this 'Doctor'."

Meanwhile…

In a place that exists outside the physical world there lays a bright light surrounded by darkness with a long Table in the center of it. It is the meeting place of Gendo Ikari, Keel Lorenz and, the thirteen other anonymous members of the SEELE Council who appear only as numbered monoliths. Here only three of them meet in secret with there cybernetic benefactor.

"Why have the three of you called me, Gaghiel has been dispatch to reclaim the embryo so, there is no need to panic even if the fleet has two operational Evangelions, to my knowledge only Unit 05 is capable of undersea combat." Keel Lorenz stated with assurance.

The raspy voice of SEELE-13 replies "Forgive me Chairman but he…" "It is not the Evangelions I am concerned about but certain personnel within the fleet." The synthesized voice of SEELE-14 said interrupting.

"The UNIT fleet that is transporting the Evangelion units has a commander that I have faced once before and despite the all years that have passed since, I have no doubts that his defiance to the inevitable remains the same." "But, it is the more recent premonitions of my associate that has me the most concerned." He finishes

"You really don't expect me to believe the prophetic insights of that malfunctioning tin can and on that note how did that… thing get a place on the council in the first place?." Keel said in disgust.

Not soon after Keel said this, the monolith of SEELE-15 spoke in his slightly garbled voice; "He is coming, the three-fold man he dances in the lonely places; oh wise counsel this I have foreseen, the Doctor is coming. Neh hah hah hah hah!" he cackled insanely.

"Do not forget he is the one who foresaw the downfall of his and fourteen's predecessors; Henry van Statten and Richard Lazarus, as well as the death of 'Harold Saxon'." SEELE-13 replied.

"It's of no consequence even if Gaghiel were to fail which is unlikely we still have our contingency plans which will ensure the scenario succeeds." Keel said with confidence as his image vanishes from the meeting room.

"Speaking of contingencies, what of our own?" Thirteen asked to Fourteen.

"The Crucible is at sixty-eight percent completion and is projected to be finished ahead of schedule however, if the power readings on the life form are correct than the long range Trans-Mat may be unnecessary and, what of the technology salvaged from the Torchwood Tower?" Fourteen asks as his monolith transformed.

"The first thirty-thousand units have been completed with another ninety-thousand to be ready by the time the Crucible is completed also, the frames for the first new model mass-production Evangelions have been prepared." Thirteen replied.

"Excellent, soon our time will come and these fools will fall, our own scenario will be unveiled and, no one not even The Doctor will be able to stop us!" Fourteen claimed as his shadow veiled form revealed itself with only one bright blue eye on what appeared to be his forehead breaking through the shadows.

"So cold and dark" Fifteen sing-songed insanely "Fire is coming... the endless flames...".

A/N: I am not the owner of Neon Genesis Evangelion, Doctor Who, Torchwood or, The Sarah Jane Adventures.

For those of you who watch the Sci-Fi Channel or the BBC the identities of the new NERV personnel and the 4th child should be easy. Also, did I get Gendo's level of insanity right or should I tone down/up or what?

Now to answer some of the more obvious questions:

Yes, Touji will be an Eva Pilot that is kind of important for the 13th Angel storylines.

Yes, other 'Doctor Who' villains will be involved.

Till next chap, Shadowblade