So Juno gets released and everything will fall into her hands, right?

WRONG.

Unbeknownst to the Assassins and Templars Torchwood has been watching them for years and knows about the whole war going on. Not interfering really because it was human business. They've been waiting to get their hands on an Apple thinking it some alien tech. Juno getting released set off their sensors/scanners and they come running.

Basically through superior alien tech, knowledge, etc. they thrash Juno who was pretty sure humans were pushovers.

Notes:
-No specific Torchwood characters are required.
-You can add in the Doctor if you want, but Torchwood should be the main focus.
-They don't have to get Juno three steps outside the cave. Use whatever scenario you want so long as requirements are met.
-How much Torchwood knows about the animus is up to writer.

Requirements:
+Torchwood NOT aligned with either faction.
+If Templars/Assassins heard of them at all they really don't know anything about them. (much to the Templars' chagrin)
+Torchwood winning and being boss.
+Modern times. Time traveling is fine, but must start in modern.