Wesley let This is what I think should have happened at the end of the episode called ‘Angel Dark, Demon Bright’. It was in the first season of Gene Roddenberry’s Andromeda.

Recap of Episode:

The episode starts with Trance taking her first try at piloting the Andromeda through slipstream. Slipstream navigation is based on human intuition, and when the pilot is nervous it can cause unwanted results. Trance is nervous, and things go wrong. They end up at a place where ‘The Battle of Witch Head’ was supposed to have taken place 300 years ago, and they have a broken slip stream so they can’t get back to where they were until it’s fixed. Harper and Tyr tell the story of the battle of Witch Head to Dylan, since it took place after he was sucked into the event horizon.
The Battle of Witch Head was the last great battle between the Commonwealth and the Nietzscheans. There were 500 Nietzschean ships, and 100 Commonwealth ships. The Commonwealth was completely wiped out, and there was significant damage to the Nietzschean fleet. Because of the damage to the Nietzschean fleet there was a civil war directly following the battle, where each pride tried for supremacy over the others. This basically wiped out most of them too.
Then everyone learns that they have somehow traveled 300 years into the past to right before the battle. Dylan at first wants to help the Commonwealth, but Tyr convinces him it is futile. Tyr tries to convince Dylan to help the Nietzscheans. Eventually Dylan decides to not do anything because he is worried they will adversely affect the future no matter what they do. So he tells everyone the plan is to just repair the ship and go back to their own time.
Then we see Harper in on of the ship’s tunnels ‘working’ on fixing the slipstream. He is video taping himself. He says he respects Dylan’s decision to leave, but he doesn’t agree, so he is going to ‘take matters into his own hands’. He says he has blinded Andromeda’s internal systems so she can’t see what he is doing, and that he has modified some key systems to allow him to cause a ‘single cataclysmic explosion’. He says he is going to kill all the Nietzscheans with this device so the Commonwealth can win the battle and the war. Then he goes on to talk about what he want’s his statue to look like – being a hero and all.
Later Trance finds Harper’s device and takes it to Harper to ask him about it. She says she knows that Harper plans to use it to kill thousands of Nietzscheans. Harper acknolodges that she is right, and wants her to give it back. Trance says no. Harper tries to reason with her by saying ‘I lived on Earth through the Nietzschean raids, and Magog attacks. Trough the famine and the plagues, but the Nietzscheans were the worst because basically they are just humans and no one beats humans for plane nastiness. Crucifixion, the electric chair, the guillotine. Any future is better than letting the Nietzscheans win.’
Trance says that he could end up killing everything in the nebula including the Commonwealth ships.
Harper says he is okay with that.
Trance says she’s not, and she runs off with his device. Harper chases her.
Next we see Trance running onto the bridge where Dylan is. She shouts, “Help he’s trying to kill me!”
Then we see Harper run in after her. He looks at Dylan and says, “I can explain.”
Next we see Rommie and Harper walking down the hall. He says, “Rommie can’t we at least talk about this?”
Rommie has the ship zap him on the butt with some kind of electricity. (Yes that really happens in the show)
He yells, “Ooww.” Then he says, “Ya know I can find my quarters on my own, thank you.”
Rommie says, “I’m not guiding you, I’m guarding you.”
Harper says, “Don’t be like this Rommie. I was trying to stop the Nietzscheans from conquering earth.”
Rommie says, “Harper if I rearranged your internal organs and tried to force you to violate your most important moral imperatives how would you feel?”
Harper says, “It actually sounds kind of fun when you say it”
They get to Harper’s room and he steps in while Rommie stands outside the door and says, “Now is not the time for humor. Seamus Harper you are confined to quarters until further notice. Feel free to rearrange the furniture to your hearts content. I recommend against making yourself invisible to me again. I might forget you ever existed and you could starve to death.”
The door closes.

Tyr and Becka work on and fix the slipstream. They are about to go back to their own time, when a bunch of Nietzschean ships appear. The Andromeda hides in some clouds. Rev Bem says his scanners are picking up 1500 ships instead of the 500 that history tells everyone there is supposed to be.
Dylan thinks they must have changed history already with Harper’s device and used it to kill the 1000 extra Nietzschean ships. He talks to Rev Bem who says he thinks it is ‘the Divine’ and fate who have brought him here to this point in time to do what needs to be done. Dylan tries to argue and asks how it could be right to kill 100,000 people and 1000 ships. Rev says more stuff about the Divine and convinces Dylan he should use Harper’s device.
Dylan says to Rommie, “Let Harper out of his quarters. We will be using the device.”
Then we see Dylan and Harper talking while Harper is holding the device. Dylan says, “Well?”
Harper says, “Well, it’s really nice that you finally decided to kill the bad guys and everything, but it’s too late.”
“How so?”
“Well this isn’t exactly a precise weapon. The idea was to rig it before they arrived when we could predict their exact location, but now…”
“They’re scattered all over.”
“Exactly. Which means it’s not going to work unless you can get them all to politely line up to be incinerated.”
“I’ll see what I can do.”
“What?”
“You get it working.”

Soon we see Dylan on the bridge with everyone but Harper. He says “Harper.”
We see Harper in the tunnel again video taping himself. He says to the camera “Finally Harper’s plan put into action.”
Dylan says, “What was that?”
“Uh…Ready.”
They bring the Andromeda out of hiding to get the Nietzscheans to follow them.
Rommie says, “We’re almost there.”
Dylan shouts, “Harper!”
Harper still video taping says, “Harper saves the world take one.”
Rommie says, “The fire controls are to command. It’s all yours Dylan.”
Dylan says, “I am become Death. Destroyer of worlds.” Then he fires.
Two thirds of the Nietzscheans are killed. 1000 ships and 100,000 Nietzschean people.
We see Harper watching the destruction on a little screen. He smiles, and then it fades into a sad, uncertain look. He says in a sad quiet voice, “We win.” And then he turns the video off.
The ship goes to slip stream, and they end up back in their own time.

This is what I think should have happened after that:

Dylan knew he would have to talk to Harper, and he wasn’t sure what he was going to say or do about Harper’s behavior. Dylan thought, ‘Four months ago,…..no it was really 300 years ago, I would have had a full crew, and I could just toss Harper in the brig for the rest of the trip. Then he would have been court marshaled when we got back home. But things are different now. I only have five crewmembers, well six including Rommie, and I need them all to be working. Hell, I wouldn’t even have Rommie without Harper. In fact Harper is brilliant, and he does his job very well. Better than any engineer I’ve had in the past, but that’s also the problem. He knows he’s the best, and he doesn’t mind telling everyone. He also knows I need him, so he thinks he can pretty much get away with whatever he wants. Like when I let him out of his room, he had the nerve to use a condescending tone when he told me it was good that I ‘finally agreed to kill the bad guys’. I need to find a way to get through to Harper. A way to let him know that I’m the one calling the shots, and that Harper going off to do his own thing – especially when that thing will kill thousands- is just not acceptable.’
As Dylan was thinking, he was walking towards Harper’s work area. As he got close he overheard Harper muttering, and he was surprised at what he heard. It was guilt.
Harper was in his work area pretending to work on something, but really he was thinking about what he had done, and talking to himself. He said, “Stupid Nietzscheans. Dumb time travel. Why did we have to be there? I know, I know, so that boy genius, namely me, could try to wipe out the Nietzschean people. Well, I was just evening out the score. Of course I didn’t know that when I built it, I just wanted the Commonwealth to win. Is that so awful? Why is that so awful? Dylan did it in the end, so maybe it isn’t so awful. Except that it is. Why is it that I can think of all these wonderful things to make, but I don’t think through what I do with them? Sometimes I hate me.”
Dylan, who had heard all of this, chose that moment to clear his throat to alert Harper to his presence. Harper jumped a little and looked guilty and embarrassed at the same time. Harper said, “Jeez Boss, don’t sneak up on me like that. I get enough of that from Tyr and Rev.”
“Harper, put down your tools, and walk with me.”
Harper stared at him for a second, and realized ‘Walk with me’ was the same phrase Dylan had used with Becka when he was going to chew her out. Or at least that’s what Becka had told him. Harper was going to try to make some excuse, but Dylan just walked out of the room to wait for Harper in the hall. Harper swallowed nervously and took his tool belt off while he thought to himself, ‘I already feel bad Dylan, you don’t need to tell me I screwed up.’
Soon he was in the hall next to Dylan who started walking. Harper fell in step beside him. Dylan said, “Harper, I think we need to talk about what happened today.”
Harper interrupted with “I really don’t think we….”
Dylan cut him off with a glare and said, “You went behind my back, and behind Rommie's back to do something you knew we would not approve of.”
Harper interrupted again with, “Yeah, but as it turned out, you needed it, so really you should be thanking me for….”
Dylan stopped and gave him an even worse glare that before, and Harper thought maybe he shouldn’t try to defend himself.
Dylan started walking again and said, “Damn it Harper, just because we ended up using your weapon, doesn’t mean it was a good idea to make it. I know Rommie has already told to you how upset she is about this, and I don’t blame her.”
Harper didn’t think this conversation was going well at all, and he said, “I apologized to Rommie.”
Dylan said, “Well at least that’s a start, but I think she’s going to have problems trusting you for a while, and so am I.”
Dylan stopped, and Harper realized they had walked to Dylan’s quarters. Dylan walked into his room and motioned Harper inside. Dylan had a couple of chairs and a table in his room. He took one seat, and gestured for Harper to sit down in the other. He said, “I want you to know that if I had a full ship, I would put you in the brig, and leave you there until we got back to port where I would have you court marshaled.”
Harper just stared at him with wide eyes and then he recovered and said, “That would be a crappy thing to do to. I’m glad you don’t have a full ship.”
Dylan chose to ignore that, and went on with, “Since I have such a small crew, and only one engineer, I can’t afford to do that. I need you working, but I also need to be able to trust you.”
Harper started to tell Dylan he could trust him, but he knew he couldn’t make it sound convincing even to himself. Dylan could trust him to protect the other people on board, and to be smart and come up with solutions to any engineering or mechanical problems, but that was about it. Dylan was correct in thinking that Harper would do what he wanted to do when it came to other things like taking vacations, doing things to make money, or getting revenge on people who had wronged him and his family.
Dylan saw Harper thinking, and could almost tell what his train of thought was. He said, "Would you have done this kind of thing to Becka behind her back?”
Harper without thinking said, “No way!”
Dylan was a little surprised and said, “Why not?”
Harper squirmed a little in his seat, and tried to come up with a convincing lie. He said, “Because she is like my family, and she would have gone along with it anyway.”
Dylan responded with, “I don’t believe that, and I don’t think you do either.”
Harper stammered a bit and said, “Well, too bad, because that’s all I have to say about it.”
Dylan said, “Well, if you would please stay here, I am going to go talk to Becka for a minute and….”
Harper interrupted with a loud “No!”
Dylan looked at Harper with a disapproving frown and said, “Excuse me?”
Harper said, “Okay, okay. I wouldn’t have done it to Becka, because….because she would have kicked my ass.”
Dylan looked at Harper funny and said, “Really?”
Harper blushed and said, “Well,….Yeah.”
Dylan said, “What exactly do you mean by kicking your ass, and how many times did she have to do it before you listened to her?”
Harper got defensive and said, “Why does it matter! Just have Rommie ‘escort’ me to my room again and leave me there for a while!”
Dylan said, “You stay right here.”
Then before Harper realized what had happened Dylan was gone. He tried to go after him, but found that the door wouldn’t open. Harper said, “Rommie, the door won’t open, will you get it for me please?”
Rommie’s voice said, “Dylan has asked me to keep you in his room until he gets back.”
“I could short the door.” Harper retorted.
Rommie replied calmly, “And I can zap you again.”
Harper sighed, and went back to his chair to wait. He hoped and prayed that Becka would keep her mouth shut, but he didn’t know if she would. He thought she would probably take a dim view if him going behind Dylan’s back even if she did agree with killing the Nietzscheans.

Dylan found Becka in the Maru doing some repairs. He said, “Becka, a word please.”
Becka said, “Sure Dylan. What can I do for you?”
Dylan said, “Short form: you know what Harper did, I don’t have the time to waste putting him in the brig, or confining him to his room. I asked him if he would have gone behind your back, and he said no. When I asked him why he said you would ‘kick his ass’ if he did. I want to know what that means exactly.”
Becka looked at Dylan for a few seconds trying to decide whether she should tell him or not. She new Harper wouldn’t like it, but she also knew Harper probably needed to realize Dylan was the boss on the Andromeda. She didn’t want him to get kicked off, because she would have to go with him, and this was the best thing they had going for them right now. She decided to tell the truth. She said, “Well, I took Harper aboard when he was sixteen, and he didn’t have much experience with following the rules.”
Dylan nodded. Becka continued with, “I don’t know of an easy way to say this, so I’m just going to tell you. When he didn’t follow my orders I spanked him.”
Dylan looked shocked. He said, “You…..what?”
Becka said, “He was just a kid Dylan. It was just him and me, and I didn’t know what else to do. He had to learn to follow orders, and I’m pretty impatient. He also needed a family, so I became that for him, and to be honest, I needed him as my family too. But that was like ten years ago. He learned pretty quick not to cross me. We’re still family, but we’re also friends now. Stop looking at me like I’ve got another eyeball in my forehead!”
Dylan smiled, “Sorry, I’m just having trouble……picturing…no!….I mean…..taking this in.”
Becka laughed a little and said with an evil smile, “Over my lap with a hairbrush.”
Dylan got very red and said, “Well….Thanks…..for the information…..I’m sure it will be….useful.”
Dylan turned and walked away quickly. His mind couldn’t help but picture what Becka had said. He shook his head to get the image out. He started to slow down when he got close to his room. He stood outside his room for a full fifteen minutes thinking about what he had learned. The more he thought about it, the more he thought it might be the best solution. Harper wouldn’t miss any work. He would hopefully learn that Dylan was in charge, and that he couldn’t just go behind Dylan’s back when he wanted to do something Dylan wouldn’t approve of. And maybe a little fear of consequences was something Harper needed. Dylan had never spanked anyone before, but his dad had spanked him a couple of times, so he knew the general routine. He decided to do it, and said, “Rommie, privacy mode.”
Rommie’s voice said, “Could I watch? He did rewire me with out telling me.”
Dylan said, “Rommie, it wouldn’t be right. Privacy mode.”
Rommie’s voice said, “Aye Captain, privacy mode engaged.”
Dylan shook his head at the ‘aye captain’ bit, and went into his room. He saw Harper jump up at the sound of the door opening. Harper looked distinctly more nervous than when Dylan left him. Once the door closed behind him he looked directly at Harper and said, “She didn’t exactly ‘kick’ your ass did she?”
Harper put his head in his hands as a blush crept up his face. He moaned and said, “Bekca how could you.”
Dylan said, “I think she thought it would be a good tactic for me to use.”
Harper’s head shot up and he said, “No Way! That was years ago. She doesn’t….do that any more.”
Harper could tell Dylan’s mind was made up because he looked very stern and said, “She hasn’t had to for a long time, but it looks like I do.”
With that Dylan grabbed Harper’s upper arm and dragged him towards a chair with him. He sat down and kept a hold on Harper’s arm when he said, “Drop your pants.”
Harper said, “NO!”
Dylan shook his head and said, “We can do this the hard way, or the easy way, but either way it’s going to happen.”
Harper stared at Dylan for a few seconds, and as Dylan reached a hand towards Harper’s pants Harper quickly unbuttoned and unzipped his pants before Dylan could.
“Shit.” Harper said as his pants fell to the floor.
Dylan pulled Harper over his lap and started to spank him. Harper yelled and tried to make things harder for Dylan by thrashing around. Harper couldn’t believe he was back in this position after so long. He thought ‘I’m twenty eight for Christ sake.’
Dylan stopped after a few minutes and said, “Now that I have your attention, I want you to tell me why I’m spanking you.”
Harper thought, ‘Crap, did she tell him everything, or is this just Dylan being Dylan?’
Harper was mad and said, “Because you’re bigger than me and you can.”
Dylan didn’t like this answer at all, so he pulled down Harper’s boxers and said, “Wrong answer.”
Dylan started the spanking again, and didn’t stop until Harper was yelping more from the pain than from the indignation. Once he stopped he said, “Let’s try again shall we? Why am I spanking you?”
Harper thought about it, and decided it would be best to just tell Dylan what he wanted to hear, so he could save his butt. “Because I went behind your back to do something that I knew you wouldn’t approve of, which is kind of like lying, and makes it so you can’t trust me.”
Dylan was surprised, but pleased that Harper got it all. He thought this kind of question must not be new for Harper, and thought Becka must have done something similar. “Very good.” He said.
Then Dylan started spanking Harper harder. Harper yelped and soon he was kicking his legs. He refused to beg, but after trying to fight it for a long time he did start to cry. Dylan could tell when Harper started to cry, because the struggles stopped, and Harper lay still over his lap. He decided they were done. He pulled Harper’s boxers back up and stood him up. He said in a kind voice, “Okay Seamus, we’re done here. You can put your pants back on.”
Harper tried to stop crying, and he had succeeded by the time his pants were back on. Then Dylan handed him a tissue for his face. He took it and blew his nose. Dylan put an arm around Harper’s shoulders, and said as he started towards his door, “I hope we don’t have to do this again Mr. Harper. Why don’t you take the afternoon off, and relax in your room for a while. I’ll see you at dinner.”
Harper nodded but didn’t say anything. He walked slowly and painfully to his room. He took off his pants and lay on his stomach on his bed. He was almost asleep when he heard a knock on the door. He pulled his covers up and said, “Come in.”
Becka came in, and said, “How are you Harper sweetie.”
Harper glared and said, “Don’t you ‘Harper sweetie’ me! I can’t believe you told him! You suck!”
Becka came over and sat beside Harper on the bed and started to rub his back in soothing circles while she said, “I know you’re mad, but I think you deserved it, and I bet you think you deserved it too. You need to follow Dylan’s orders, the same way you follow mine. I don’t want us getting kicked off the ship. Sleep now. Things will look better after a couple of days.”
Harper listened to her, and he even knew there was some truth in what she said, but he didn’t comment or show her that he had heard in any way as she left the room. He soon fell asleep.

Harper woke up and rolled to his back. He quickly rolled to his front again remembering what had happened. He groaned and looked to see what time it was. He took a quick shower and got dressed. He went to join everyone for dinner, because he knew it would look suspicious if he didn’t show up. He was the first one there, so he got a sparky cola and drank it standing up. As soon as he heard voices he sat down with a wince and tried to look like it didn’t hurt.
Harper gobbled down his food as soon as the drone set it in front of him. Both Tyr and Trance commented on his gross eating habits, but it didn’t slow Harper down. Then, well before anyone else was done, he excused himself to go do some work.
Later that evening when he was working in the shop Dylan came by. He looked up and said, “What can I do for ya Boss?”
Dylan looked a bit awkward and said, “I….I just wanted to make sure you were okay.”
Harper smiled and said, “Well no, I’m not okay, but I will be in a couple of days.”
Dylan thought it was a good sign that Harper was able to smile and talk about it. He said, “I just wanted to tell you I forgot something before. Something my father always told me – you’re forgiven Harper. Just don’t let it happen again.”
Harper said, “Thanks Dylan, and to tell you the truth, I kind of feel better now. I was really mad at myself before, but now I can let it go. Becka was right – damn her, so no hard feelings. It isn’t like it’s my first time,….even if it’s been a while.”
Dylan smiled and patted Harper on the shoulder as he left the room. He thought that was the most mature thing he had ever heard Harper say. He still felt strange about the spanking, but he couldn’t argue with the results. He would keep it in mind for the future.