Based on the events in 'Out of His Head' (s1e14).
The cure took some time to work but, by the time the children were back from school the next evening, Ratchet finally allowed Optimus to get up from the med berth. Everyone gathered near the medbay, except Liliy who was sitting on the stairs watching with a smile, and cheered and clapped happily as Ratchet pulled the taller mech to his peds and helped him stand upright.
"Please," said Optimus, still leaning on Ratchet a little. "Reserve the hero's welcome for my physician." Ratchet smiled up at him. "And my scout." He gestured to Bumblebee.
The gang turned to look at Bumblebee, still clapping. Buzzing, he rubbed the back of his helm, a little embarrassed by the attention.
"Way to go, Bee," cheered Raf.
Bumblebee took a bow. As he straightened up, there was a hitch in his movement and he stood frozen for a few seconds. No one seemed to notice but Liliy who frowned at the way Bee stared straight ahead at nothing. She was not sure why but she had a bad feeling that patch may have had a negative effect on the scout. Then Bee shook his helm and bowed again.
"Well then," said Ratchet. "I hate to break up the celebration but it's time for you children to go home."
"What?" whined Miko. "Why? We haven't gotten to play yet."
"Because it is getting late and Optimus needs some more rest. You can play tomorrow."
"Fine. Come on, Bulk."
The guardians transformed to take their charges home.
The next day, Liliy hung out on the first tier next to the medbay while Ratchet performed a check-up on Optimus. She was interested in the Prime's condition but her real reason for being there was to keep an eye on Bumblebee who stood nearby with Arcee.
"I wouldn't advise anything strenuous, Optimus," Ratchet commented as he finished the check-up, "but it appears that your systems have fully recovered from the Cybonic Plague."
"Thanks to your medical expertise, old friend," Optimus stated as he stepped out of the medbay's containment area.
"It was your scout who braved unknown territory to locate the cure," countered Ratchet, turning to look at Bumblebee.
"No. No. I'm not that great," he beeped, waving his servos frantically.
"Lucky for us Megatron was still alive," said Arcee.
"Did you seriously just say that?"
"Yeah. I actually said that."
"What matters is that you are on the mend, Optimus." Ratchet looked up at the taller mech. "While Megatron-"
"We really don't know what happened to him."
"He's right," added Arcee. "I did my best to finish Megatron's story. Just couldn't stick around long enough to see how it ended."
While Arcee was speaking, Liliy again witnessed a hitch in Bee's movements and his optic irises narrowed. Then he suddenly turned and walked into the hallway, his posture oddly stiff. Liliy, curious, quickly followed after him. He stopped a little ways down the hall. He examined his servos, flexing his digits as if he was testing them.
"Bee?" Liliy asked softly as she came around to his front.
He did not appear to hear her. Instead he stared straight ahead with a dark, angry glare. This uncharacteristic, unseeing gaze startled Liliy. She carefully approached his ped.
"Bumblebee?" she inquired a little louder this time as she reached out and touched the metal on his ankle.
Bumblebee jerked slightly and looked down at her with a surprised yet clear expression.
"Are you ok, Bee?"
"Of course," he chirped, giving her a thumbs up and then continuing down the hall.
Liliy watched him go, not at all convinced that he was.
The next time Bumblebee spaced out was that afternoon when the children came to play. Bulkhead and Bumblebee were playing a game of 'basketball by way of Cybertron' as Miko called it. Bulkhead had just made a basket so he passed the ball, made out of scrap metal, to Bumblebee.
"Come on, best two out of three," the wrecker said.
Bumblebee caught the ball and moved toward the hoop. He dodged around Bulkhead who was trying to block him.
"Bee," cheered Raf. "You're in the clear. Dunk it, Bee."
But Bumblebee just slowed to a stop in front of the hoop and his expression went blank.
"Bumblebee," Bulkhead said after the scout was still for a few seconds. "Quit hogging the ball."
No one but Liliy was quick enough to notice the angry glare on Bee's face as he suddenly spun and launched the ball at Bulk's helm. Quicker than his frame led one to believe it was, Bulkhead ducked and the ball crashed into the rockface wall behind him.
Miko blew her whistle. "Aaaa. Flagrant foul," she cried.
"Dodgeball by way of Cybertron," suggested Jack.
"Bee," Bulkhead corrected the suddenly confused scout. "Hoop's over there."
He pointed at the big metal ring attached perpendicular to a metal backboard on the catwalk.
"I'm really sorry, Bulkhead. I don't know what came over me."
"Bee, you ok?" asked Raf.
"I'm fine. Let's go again." He held up three digits.
"Yeah," agreed Raf, though he wasn't totally convinced. "Three out of five."
The game finished without another hitch. Bumblebee beat Bulkhead; five games out of seven.
The next morning, Liliy's phone started ringing, waking her up. She rolled over and picked it up, frowning at the display before answering.
"Raf? Is something wrong? Shouldn't you be at school right now?"
{Bumblebee never came to pick me up. And his commlink's off again. Is he there at the base?}
"I haven't seen him but let me go down and check the back rooms."
Liliy got up from her sleeping bag and went to the elevator.
"Hey, Raf. Has Bee been acting weird lately or is this the first time?"
{Now that you mention it… Yes, he has. Yesterday, when he picked me up from school, he just kinda sat there until I asked what was wrong. He said it was nothing and drove to the base like normal. But then he threw that ball at Bulkhead.}
"Yeah. I saw that. A couple of times before that I saw him space out. He has definitely been acting a little weird since-" Liliy stepped out of the elevator and spotted Bumblebee.
He was over by the medbay. He stopped to look at something on Ratchet's workbench, when his frame jerked slightly before it stiffened. His optics narrowed. Stepping toward the workbench, he reached out and picked up a tool that was sitting there. He held it for a second before he suddenly crushed it in his fist while glaring harshly at nothing.
Liliy just stared, open-mouthed, not hearing Raf asking her what was wrong through her phone.
"Bumblebee!" Ratchet's voice exclaimed from the hallway entrance behind the scout.
Bumblebee's optics widened in surprise and he turned to the medic.
"I needed that!" Ratchet cried upon seeing the broken tool.
"Whoops," beeped Bumblebee, looking down at the tool.
"What has gotten into you?"
"I don't know. I keep seeing visions of Megatron's face inside my head."
"You're seeing Megatron's face?" Ratchet sounded concerned.
"Raf," Liliy said suddenly, drawing the attention of the two Bots. "I found Bee. He's here at the base. How would you feel about skipping school today? I think Bee could really use your support right now."
{Is something wrong?}
"We don't know yet. I can send you a bridge if you want."
"Liliy, school is-" Ratchet stopped speaking when Liliy shot him a glare. He waved it off and turned his attention to Bumblebee.
{If Bee needs me, I'll come.}
"Thanks, Raf. I'll send you that bridge right now."
Liliy hung up and hurried over to the computer. She punched in the coordinates of Raf's phone and opened the ground bridge. Raf appeared in the portal. But before he could ask what was wrong, Optimus, Arcee, and Bulkhead rolled in and transformed.
"Rafael," Optimus inquired upon seeing the boy. "Shouldn't you be at school?"
"Bumblebee never picked me up for school. And when I call Liliy looking for him, she said he was here and something might be wrong with him so she bridged me over."
Optimus looked up at Liliy in surprise.
"Ask Ratchet," Liliy informed him. "He already started an examination."
Ratchet was in the medbay, having Bumblebee step into the containment area. Optimus moved over to the medbay. Raf followed, running to keep up with him.
"Ratchet, is something wrong Bumblebee?"
"Bumblebee's complaining of intermittent visions," explained Ratchet as he had Bumblebee power down. "Waking nightmares if you will. Ever since he and Arcee came back from the Nemesis."
"But you said Bee was fine when you checked him over," said Raf. The boy stood at Bumblebee's peds. Liliy came over and stood next to him.
"Physically," replied Ratchet. "But the experience he endured seems to be having a temporary effect on his psyche."
"That kind of explains his odd behavior lately," said Liliy.
"This induced power-down," continued Ratchet, "should force Bumblebee's mind to rest and recover."
The base commlink beeped. Ratchet answered it on the monitor in the medbay. Agent Fowler appeared on the screen. Everyone gathered around to listen.
{Prime. You spot any Decepticons wearing hula skirts lately?}
Liliy actually chuckled aloud at the mental image.
"No, Special Agent Fowler," answered Optimus. "Why?"
{Cause I was hoping you had a lead on the Cons that busted into the Kauai Naval Observatory. Place looked like it was hit by an army of wrecking balls.}
"Why would Cons break into an observatory?" asked Arcee.
{Does the Heuck Nigoghossian ring any bells?}
"The space telescope," answered Raf, who stood between Liliy and Optimus.
{As of last night missing its primary lens.}
"It's difficult to guess Starscream's intent without knowing where the lens has been taken," said Prime.
"Does something like that have a tracking device just in case it does get stolen?" asked Liliy.
{Yes, it does. I have already acquired the frequency and activated the tracker. You'll never guess where it's been taken.}
The main console beeped and a map of the top of the world popped up, with the beacon indicator right in the center.
"The Arctic?" asked Arcee skeptically as the Bots moved out of the medbay and over to the main console. Raf and Liliy ran up to the platform with the computers to see better. "Great. Another chance to freeze our spark plugs off."
The computer zoomed in on the area. The beacon appeared very close to an energon deposit.
Bulkhead whistled. "That's an ND-7 class. Biggest unmineable energon deposit there is."
"Unmineable," followed Optimus, "until Starscream melts his way down to it."
"With the help of the lens," added Arcee.
{Melting a glacier that size would cause sea levels to rise and demolish coastal cities.}
Optimus got that decisive look. "Autobots, time to roll out."
A while later after the Bots had left, Liliy found Raf talking to the powered down Bumblebee. She leaned against the containment area's doorframe to listen. He was telling him about his family.
"Rafael," said Ratchet, walking over, "I'm afraid Bumblebee can't hear you in power down mode. It's getting late. Why don't I bridge you home to your family?"
"Because I told Bee I'd stay. He's family too."
"Don't be ridiculous. You're not even the same species."
"That's being related, Ratchet," said Liliy. "It's not the same thing."
"Yeah," agreed Raf. "Here. I'll show you." He pulled out his phone and showed them a picture. "This is my family."
Ratchet knelt to get a closer look. "Hm. Yes. Very nice," he muttered.
"Very large. Sometimes I can shout and no one hears me."
"Yes, yes," replied Ratchet, not quite listening himself.
"But Bumblebee always listens," Raf continued, surprising Ratchet. "And I can understand him. I'm not sure why, but I do."
"Reminds me of my family," said Liliy. "I had a large one once but they are all gone now. So I made a new one. A bunch of family-less rabble banded together. We're not related but we consider each other family. None of you are related but you consider the other Autobots as your family right, Ratchet?"
He looked a little taken back by the question but he managed to stutter out, "I s-suppose." He turned away and missed the knowing smiles that passed between the two humans.
Later, Liliy had moved up to her chair and Raf had his laptop out near Bee.
"Rafael, I'm going to the supply vault to see if I can find parts to repair this," Ratchet said, holding the tool that Bumblebee broke. "You know what that means?"
"Don't touch anything," answered Raf.
Ratchet nodded. "Same goes for you, Liliy." He looked over at her.
"Yes, Ratchet."
He disappeared down the hall next to the medbay.
Raf was talking to the yellow bot again when Bumblebee suddenly came online. He stepped out of the containment area.
"Bumblebee, wait!" Raf shouted, getting up to chase after him.
Liliy got up too but she stopped at the sight of the angry expression on Bumblebee's faceplates. Bumblebee went to the bridge controls, entered some coordinates, and left via the bridge.
"Bumblebee," Raf called after him as the bot disappeared.
"What did you do?" Ratchet asked, having come back when he heard Raf shout.
"Nothing. Bumblebee just got up and…"
"He was in power down. Where does he think he's off too?"
Ratchet went over to the controls as the ground bridge shut down. Raf and Liliy joined him. He found the coordinates that Bumblebee used.
"These are the coordinates for the site of our previous battle with Megatron's undead."
"Undead?" asked Liliy.
"Megatron used dark energon to raise Cybertronian corpses to fight Optimus."
Liliy looked horrified.
"Maybe we should call Optimus," suggested Raf.
"Optimus is busy preventing a polar ice cap from melting," replied Ratchet. "We need to handle this on our own."
He reactivated the ground bridge. Just as Ratchet was about to go out, Bumblebee came back through.
"Bumblebee… What have you been doing?" He caught Bee's arm to see what he had in his servo. "Dark energon?" he asked incredulously.
Bumblebee, glaring, suddenly punched Ratchet in the face, sending him crashing into the concrete platform next to the bridge controls.
"Bee, what are you doing?" asked Raf as Bumblebee stepped menacingly closer.
Liliy grabbed the Raf around the waist, lifting him and backing away from the mech as he reached out a servo to grab the boy.
"Stay away from him," she hissed.
Raf was surprised by the threat in her voice.
"But, Liliy, Bee won't-"
"That is not Bumblebee."
The mech glared for a moment and then reached over to the controls and opened a new bridge. After Bumblebee left, Liliy let Raf go and he ran over to see if Ratchet was alright.
The medic groaned as he pushed himself up.
"Ratchet, are you ok?"
"I'm fine. More importantly, is Bumblebee?"
"Liliy said that wasn't Bee."
Ratchet looked surprised and turned to her. "What do you mean, Liliy?"
"I could tell. The look in his optics. It wasn't him. Perhaps it was Megatron. The cortical psychic patch could have acted like a two way path and the Con could have taken over his mind. Because that was not Bumblebee."
The medic looked shocked. "You're right. Why didn't I think of that before? Megatron was the only one who knew about the dark energon. And now he has bridged to almost the exact coordinates Optimus used," he said, checking the controls again. He opened the bridge. "Stay here."
"No. Bee needs me," argued Raf.
"Go ahead," Liliy reassured him. "I'll man the ground bridge."
"Alright. Come on, Rafeal."
The medic put the boy on his shoulder and left. As soon as the bridge shut down, Liliy pulled out her phone and hooked it up to the computer. A chat window opened up.
[I have the base to myself for a little while. Anyone want to chat?] she typed. She smiled cheerfully as the window was instantly flooded with replies from most of her 'boys'.
Some time later...
{Liliy. We need a bridge.}
Liliy, startled awake by the comm, fell out of the chair in front of the computer.
{Liliy?}
"Yeah. Sorry. One ground bridge coming right up."
She opened a bridge.
"So what happened?" she asked after everyone came through.
"Unfortunately, the lens was destroyed," answered Optimus.
"And Megatron is back in action," added Arcee.
"But we saved the day in the end," Bulkhead commented.
"And we have Bee back." Raf smiled down from the yellow bot's shoulder.
"Liliy, thanks for looking out for Raf while I wasn't myself," Bee chirped.
"No problem, Bee. That's what family's for," Liliy replied, winking at Raf.
"Alright, Bumblebee, Optimus, over to the medbay," said Ratchet. "You both need check-ups after all the excitement today."
"Another one?" complained Bee.
Everyone laughed.
Yeah... so I have come up with an idea for a prequel/origin story for the CRC. I may or may not start writing it soon.