So Thor takes Loki back to Asgard. Odin isn't exactly pleased to see his adoptive son return. However Loki could have his... uses.
Loki is referred to by many names, one of which is 'the Mother of Monsters' due to the fact that many of his children were more creature shaped than humanoid shaped. Fenrir, Sleipnir, Jormungandr, Hel, you get the picture. In any case Odin thinks that having more such creatures could be beneficial, especially if he can control them.
He proceeds to lock Loki up and occasionally throw powerful creatures in with him and hope that it will work out as planned.
Cue the non-con!
Eventually Loki is with child, and he knows the moment it's born Odin will take it from him. He can't bare to loose another of his children to Odin so he makes an escape. He manages to slip back to Midgard and this sets off some SHEILD alarms pretty damn fast. The Avengers find him in a pretty bad way and no one's really sure what to do. They take him back to HQ and after some tests find out he's pregnent. Loki begs them not to let Thor take him back, and after much consideration they agree to this.
Eventually the creature is born (your call, not human-y though), and all the Avengers are sorta like 'Ummmm, wtf?' and Loki is all 'omg isn't he/she/it perfect! *bliss*'
ANything after that is your call.
Bonus points for Bruce getting along with/being protective of Loki, Loki getting his lips sewn shut (cause Norse mythos was a lot meaner to him than the script writers), and Loki dealing with panic attacks (due to fear to Odin/going back to Asgard/not being able to breath through his mouth).

chapter 1

A storm was raging. Huge black clouds blocked out what little light the stars offered, their bulky forms an intangible yet oppressive weight. The Avengers were assisting with clean up after their most recent run in with HYDRA. A nasty battle, but it was won now, and the damage to the team was minor. The same could not be said for the surrounding area. Steve was helping remove rubble from the immediate vicinity as the rest of the team fanned out for further damage control. The fighting that day had mostly been contained within several blocks and so their work was nearly done. Steve was on his final pass through the block when he heard a familiar shout. Images filled his mind of a green-eyed madman, if he was right there was no way this was going to be a good thing. After brief contemplation he decided to investigate, better safe than dead when the god of mischief was involved.

Following a series of cries that sounded more and more like the god in question than any potential victim, he ended up near a darkened alley not far from where the main fighting had taken place. Deciding that it might be prudent not to go in alone he quickly checked in with the rest of the Avengers. "I'm investigating an alley over here on 56th street. I think I may have heard our old friend Loki."

"I thought Thor had taken him back to Asgard?" Tony responded over the radio.
"You're not the only one. Get here as soon as you can."

"Got it." After Tony turned off the comm link Steve turned back toward the alley. It was twilight, but with the rain hampering his vision it was still difficult to see what exactly was happening. At the sound of another scream and the crash of metal the Captain rushed down the alley without a thought as to what he might encounter.

Loki was running, or at least the best he could manage being several months pregnant. The weight was visible, but apparently not a deterrent to the HYDRA agent currently chasing him down. Between the sense of panic and the constant barrage of rain his coordination was shot and he only avoided falling through sheer luck. Even with Loki's panic-fueled efforts that man was gaining fast, and when he crashed into a trashcan any chance of escape was lost. The man was upon him in an instant.

He hated to call out but his current position didn't offer him much choice. "Help!" Loki screamed eyes rolling as he searched for an escape route.

"No one is going to be coming here to rescue you. It's just you and-" the man was interrupted as a fist collided with his face.

"Didn't your mother ever teach you not to hurt a lady?" The Captain quipped. He looked down at the cowering form of the god. "Although on second glance you are definitely not a lady. What are you doing here Loki?" the Captain turned a scowl on Loki.

Before Loki had a chance to respond Tony dropped out of the sky shortly followed on foot by Clint, Natasha, and Bruce.

"So where's Loki? Did you scare him off?" Tony asked looking at Steve. He shook his head and pointed at the cowering ball at his feet.

"He's scared, but it wasn't my doing."

"Any idea why he is here?" asked Natasha, eyeing the god mistrustfully.

"I was just getting to that." Steve turned back to Loki. "Give me one good reason why we shouldn't call Thor to haul you back to Asgard."

Loki visibly shivered at the mention of Thor and Asgard, before looking up at the Avengers standing over him. Slowly he uncurled himself revealing the prominent bulge of his stomach and responded in a weak, shaky voice, "This is why, and if you take me back to your headquarters I swear I shall tell you everything. I will even be gladly confined in one of your cages if you wish. Just do not call my brother," He cast his gaze to the ground again fear and uncertainty plain in his expression.

The Avengers were shocked by the obviously pregnant state of the god. Steve turned a dumbstruck look toward Tony and Bruce waiting for a scientist to tell him if this was normal now a days. Tony just shook his head, before responding, "It couldn't hurt to take him back; he has agreed to give us information and it's not like he is in any state to fight right now. So, any objections?" Tony looked around and seeing only shocked faces decided, "with no objections then Cap, could you carry our prisoner back to the mansion?"
"Yes, sir." Steve responded then went to pick up a significantly relaxed Loki.

"Everyone meet back in an hour in the lobby. We can discuss this further there."

Time passed quickly and the Avengers were soon assembled at Stark tower with the addition of Coulson and Fury. "How did you get invited?" Tony shot at them. He had removed his armor by this point and looked quite comfortable in a faded Iron Maiden tee.

"You expect us not to immediately know about the arrival of an insane Norse god? We've got a tracking program just for him," Fury responded with an incredulous look. Tony scowled in response.

"Since everyone is here, let's move to the meeting room. Banner is waiting with Loki so hopefully we can figure out what we are going to do about all this." Steve moved to the elevator, and everyone quickly shut up and followed.

"Why didn't we just meet there?" Jan asked before getting a look from Steve.

They entered the room to find Loki seated at the head of the table with Bruce standing behind him. His look of terror from before had settled somewhat, though he still looked as if he would startle at the slightest provocation. Fury settled swiftly into a seat and beat Steve to asking the question everyone was waiting for, "Why are you here?"

"To escape Asgard and protect my child. I'm sure that if you have done your reading you know what happened to the rest of my children."

"Why 'escape'?" Tony asked with a hint of doubt, "We all know you were sent to Asgard to face punishment, but other than the obvious, why did you need to escape?"

"Odin's punishment was something that I'm sure even you Midgardians would find repulsive. It's the reason I'm in this state." He cast his gaze down upon his stomach with a hint of sorrow and shame.

"Mind explaining what you mean by that?" asked Fury.

"I promised to tell you the whole story didn't I? Why don't I just start from the beginning and you may ask questions as I go."

"Fair enough," Steve responded. The rest of the Avengers and Fury nodded their agreement. "Jarvis, you recording this?"

"Yes, sir. From the beginning."

Loki looked up with annoyance at the robotic voice. "Wonderful to know another of my misfortunes will be recorded for eternity," he sighed sarcastically.

"Go on Loki." Fury interrupted. Loki responded with a glare before starting his story.

"It began when I landed in Asgard with Thor..."